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

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

tests
0

failures
0

ignored
1m42.09s

duration
100%

successful

Tests

Test Duration Result
exhaustiveArgumentTest[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder12893922296381744565/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null) 1.093s passed
exhaustiveArgumentTest[1](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder786102342866777495/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null) 1.595s passed
exhaustiveArgumentTest[2](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder12893922296381744565/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null) 0.997s passed
exhaustiveArgumentTest[3](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder786102342866777495/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null) 1.077s passed
exhaustiveArgumentTest[4](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder12893922296381744565/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null) 1.124s passed
exhaustiveArgumentTest[5](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder786102342866777495/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null) 1.167s passed
exhaustiveArgumentTest[6](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder12893922296381744565/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null) 1.116s passed
exhaustiveArgumentTest[7](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder786102342866777495/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null) 1.217s 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) 6.195s 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) 5.470s passed
nonTrivialLargeDataValidationTest[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf, [], false) 1.982s 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) 2.120s 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) 12.623s 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) 5.800s 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) 0.102s passed
testCanAnnotateHg38ClinvarAndGencodeV28 0.199s passed
testCanAnnotateMixedContigHg19Clinvar 0.122s passed
testCanAnnotateSpanningDeletions 0.175s passed
testCanCreateNonLocatableFuncotations 1.014s passed
testCanHandleSymbollicAlleleFuncotations 1.007s passed
testCustomVariantClassificationOrder 1.031s passed
testEColiFuncotations 0.182s passed
testEnsureDbSnpInMaf 0.096s passed
testExclusionFromDatasourceVcfToVcf 0.244s passed
testFilterParsing 0.131s passed
testFuncotatorWithoutValidatingResults[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder12893922296381744565/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null) 0.986s passed
testFuncotatorWithoutValidatingResults[1](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder786102342866777495/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null) 1.121s passed
testFuncotatorWithoutValidatingResults[2](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder12893922296381744565/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null) 1.029s passed
testFuncotatorWithoutValidatingResults[3](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder786102342866777495/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null) 1.102s passed
testFuncotatorWithoutValidatingResults[4](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder12893922296381744565/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null) 1.142s passed
testFuncotatorWithoutValidatingResults[5](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder786102342866777495/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null) 1.086s passed
testFuncotatorWithoutValidatingResults[6](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder12893922296381744565/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null) 1.025s passed
testFuncotatorWithoutValidatingResults[7](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder786102342866777495/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null) 1.070s passed
testMANESelectAnnotationDifferencesAndGencodeV43 0.443s passed
testMafCustomCountFieldsTumorOnly[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf) 0.103s passed
testMafCustomCountFieldsTumorOnly[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields_tumor_only.vcf) 0.102s passed
testMafCustomCountFields[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf) 0.125s passed
testMafCustomCountFields[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf) 0.104s passed
testManualAnnotationsCorrectness 0.112s passed
testMoreThanOneTNPair 0.096s passed
testNoSpanningDeletionWriteWithMAF 0.157s passed
testNoVariantsProduceMaf 0.095s passed
testSequenceDictionaryCheck 0.090s 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) 5.876s passed
testUserExceptionOnAlleleDepthFieldSizeOneForMafOutput 0.869s passed
testVCFColumnsArentShuffled 0.099s passed
testVCFToMAFPreservesFields 0.109s passed
testVCFToVCFPreservesFields 0.137s passed
testVcfDatasourceAccountsForAltAlleles 0.107s passed
testVcfMafConcordance[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf, /tmp/funcotatorTmpFolder6604497074802621324/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 15) 0.217s passed
testVcfMafConcordance[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder6604497074802621324/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57) 0.269s passed
testVcfMafConcordance[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf, /tmp/funcotatorTmpFolder786102342866777495/GRCh37.p13.chr19.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, false, 2057) 35.444s passed
testVcfMafConcordance[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf, /tmp/funcotatorTmpFolder8067971494638115744/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) 0.418s passed
testVcfMafConcordance[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder6604497074802621324/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) 0.306s passed
testVcfToMafHonorsExcludedFields 0.108s passed
testXsvLocatableAnnotationsHaveCorrectColsForOnlyOnePositionSpecified 0.136s passed
testXsvLocatableAnnotationsHaveOnlyOneEntryForMultiHitLocations 0.127s passed

Standard error

19:09:12.674 INFO  Funcotator - ------------------------------------------------------------
19:09:12.674 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:12.674 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:12.674 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:12.674 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:12.674 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:12 PM GMT
19:09:12.674 INFO  Funcotator - ------------------------------------------------------------
19:09:12.674 INFO  Funcotator - ------------------------------------------------------------
19:09:12.674 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:12.674 INFO  Funcotator - Picard Version: 3.4.0
19:09:12.674 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:12.674 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:12.674 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:12.674 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:12.674 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:12.675 INFO  Funcotator - Deflater: IntelDeflater
19:09:12.675 INFO  Funcotator - Inflater: IntelInflater
19:09:12.675 INFO  Funcotator - GCS max retries/reopens: 20
19:09:12.675 INFO  Funcotator - Requester pays: disabled
19:09:12.675 INFO  Funcotator - Initializing engine
19:09:12.676 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
19:09:12.677 INFO  Funcotator - Done initializing engine
19:09:12.677 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:12.677 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:12.677 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder12353274574955864394/TranscriptIdFile.txt
19:09:12.677 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
19:09:12.678 INFO  FuncotatorEngine - Transcript parsing complete.
19:09:12.678 INFO  Funcotator - Initializing data sources...
19:09:12.678 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:12.678 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:12.678 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
19:09:12.679 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
19:09:12.679 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
19:09:12.679 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
19:09:12.679 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
19:09:12.680 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
19:09:12.680 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
19:09:12.680 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:12.680 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
19:09:12.681 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
19:09:12.681 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
19:09:12.681 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
19:09:12.681 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:12.682 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
19:09:12.682 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
19:09:12.682 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:12.682 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
19:09:12.682 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
19:09:12.712 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
19:09:12.712 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
19:09:12.757 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
19:09:12.758 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
19:09:13.341 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
19:09:13.342 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:13.343 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:13.345 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
19:09:13.347 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:13.349 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:13.350 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:13.350 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:13.393 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:13.394 INFO  DataSourceUtils - 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	2025-05-19 19:09:13	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:13.394 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
19:09:13.432 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
19:09:13.432 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
19:09:13.432 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
19:09:13.440 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:13.511 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
19:09:13.511 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:13.512 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:13.512 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
19:09:13.601 INFO  Funcotator - Initializing Funcotator Engine...
19:09:13.601 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
19:09:13.601 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
19:09:13.601 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
19:09:13.602 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
19:09:13.602 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
19:09:13.603 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
19:09:13.604 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
19:09:13.605 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
19:09:13.605 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:13.605 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.36447782167650312978.vcf
19:09:13.606 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
19:09:13.608 INFO  ProgressMeter - Starting traversal
19:09:13.608 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:13.676 INFO  ProgressMeter -             unmapped              0.0                     3           2647.1
19:09:13.676 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
19:09:13.676 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:09:13.679 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:13 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2321547264
19:09:13.805 INFO  Funcotator - ------------------------------------------------------------
19:09:13.805 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:13.805 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:13.805 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:13.805 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:13.805 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:13 PM GMT
19:09:13.805 INFO  Funcotator - ------------------------------------------------------------
19:09:13.805 INFO  Funcotator - ------------------------------------------------------------
19:09:13.805 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:13.805 INFO  Funcotator - Picard Version: 3.4.0
19:09:13.805 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:13.805 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:13.805 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:13.805 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:13.805 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:13.805 INFO  Funcotator - Deflater: IntelDeflater
19:09:13.805 INFO  Funcotator - Inflater: IntelInflater
19:09:13.806 INFO  Funcotator - GCS max retries/reopens: 20
19:09:13.806 INFO  Funcotator - Requester pays: disabled
19:09:13.806 INFO  Funcotator - Initializing engine
19:09:13.807 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
19:09:13.807 INFO  Funcotator - Done initializing engine
19:09:13.807 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:13.807 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:13.808 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder2040588592329454997/TranscriptIdFile.txt
19:09:13.808 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
19:09:13.808 INFO  FuncotatorEngine - Transcript parsing complete.
19:09:13.808 INFO  Funcotator - Initializing data sources...
19:09:13.808 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:13.808 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:13.808 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
19:09:13.808 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
19:09:13.809 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
19:09:13.809 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
19:09:13.809 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
19:09:13.809 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
19:09:13.809 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
19:09:13.810 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:13.810 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
19:09:13.810 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
19:09:13.810 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
19:09:13.810 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
19:09:13.811 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:13.811 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
19:09:13.811 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
19:09:13.811 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:13.811 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
19:09:13.811 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
19:09:13.830 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
19:09:13.831 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
19:09:13.938 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
19:09:13.939 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
19:09:14.731 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
19:09:14.732 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:14.737 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:14.739 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
19:09:14.743 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:14.746 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:14.747 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:14.747 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:14.776 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:14.776 INFO  DataSourceUtils - 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	2025-05-19 19:09:14	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:14.777 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
19:09:14.840 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
19:09:14.841 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
19:09:14.841 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
19:09:14.848 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:14.849 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
19:09:14.849 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:14.849 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:14.850 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
19:09:14.980 INFO  Funcotator - Initializing Funcotator Engine...
19:09:14.980 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:09:14.980 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:14.980 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.44801755085076789149.vcf
19:09:14.981 INFO  ProgressMeter - Starting traversal
19:09:14.981 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:15.273 INFO  ProgressMeter -             unmapped              0.0                     4            821.9
19:09:15.273 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
19:09:15.273 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:09:15.274 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:15 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2686451712
19:09:15.373 INFO  Funcotator - ------------------------------------------------------------
19:09:15.373 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:15.373 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:15.373 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:15.373 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:15.373 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:15 PM GMT
19:09:15.373 INFO  Funcotator - ------------------------------------------------------------
19:09:15.373 INFO  Funcotator - ------------------------------------------------------------
19:09:15.373 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:15.373 INFO  Funcotator - Picard Version: 3.4.0
19:09:15.373 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:15.373 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:15.373 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:15.373 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:15.373 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:15.373 INFO  Funcotator - Deflater: IntelDeflater
19:09:15.373 INFO  Funcotator - Inflater: IntelInflater
19:09:15.373 INFO  Funcotator - GCS max retries/reopens: 20
19:09:15.373 INFO  Funcotator - Requester pays: disabled
19:09:15.373 INFO  Funcotator - Initializing engine
19:09:15.374 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
19:09:15.375 INFO  Funcotator - Done initializing engine
19:09:15.375 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:15.375 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:15.375 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder6937963469532498896/TranscriptIdFile.txt
19:09:15.375 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
19:09:15.375 INFO  FuncotatorEngine - Transcript parsing complete.
19:09:15.375 INFO  Funcotator - Initializing data sources...
19:09:15.375 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:15.375 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:15.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
19:09:15.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
19:09:15.376 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
19:09:15.376 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
19:09:15.376 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
19:09:15.377 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
19:09:15.377 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
19:09:15.377 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:15.377 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
19:09:15.378 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
19:09:15.378 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
19:09:15.378 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
19:09:15.378 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:15.378 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
19:09:15.379 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
19:09:15.379 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:15.379 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
19:09:15.379 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
19:09:15.398 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
19:09:15.398 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
19:09:15.444 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
19:09:15.445 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
19:09:16.023 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
19:09:16.024 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:16.025 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:16.027 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
19:09:16.029 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:16.032 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:16.032 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:16.032 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:16.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:16.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-19 19:09:16	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:16.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
19:09:16.148 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
19:09:16.149 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
19:09:16.149 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
19:09:16.157 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:16.157 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
19:09:16.157 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:16.158 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:16.159 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
19:09:16.235 INFO  Funcotator - Initializing Funcotator Engine...
19:09:16.235 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
19:09:16.236 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
19:09:16.236 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
19:09:16.236 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
19:09:16.236 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
19:09:16.237 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
19:09:16.237 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:16.237 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.32561093236100570509.vcf
19:09:16.238 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
19:09:16.239 INFO  ProgressMeter - Starting traversal
19:09:16.239 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:16.267 INFO  ProgressMeter -             unmapped              0.0                     3           6428.6
19:09:16.267 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
19:09:16.267 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:09:16.270 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:16 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2686451712
19:09:16.357 INFO  Funcotator - ------------------------------------------------------------
19:09:16.357 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:16.357 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:16.357 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:16.357 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:16.357 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:16 PM GMT
19:09:16.357 INFO  Funcotator - ------------------------------------------------------------
19:09:16.357 INFO  Funcotator - ------------------------------------------------------------
19:09:16.357 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:16.357 INFO  Funcotator - Picard Version: 3.4.0
19:09:16.357 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:16.357 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:16.357 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:16.357 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:16.358 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:16.358 INFO  Funcotator - Deflater: IntelDeflater
19:09:16.358 INFO  Funcotator - Inflater: IntelInflater
19:09:16.358 INFO  Funcotator - GCS max retries/reopens: 20
19:09:16.358 INFO  Funcotator - Requester pays: disabled
19:09:16.358 INFO  Funcotator - Initializing engine
19:09:16.359 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
19:09:16.359 INFO  Funcotator - Done initializing engine
19:09:16.359 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:16.359 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:16.359 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder15340671969053458343/TranscriptIdFile.txt
19:09:16.359 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
19:09:16.359 INFO  FuncotatorEngine - Transcript parsing complete.
19:09:16.359 INFO  Funcotator - Initializing data sources...
19:09:16.359 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:16.359 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:16.360 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
19:09:16.360 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
19:09:16.360 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
19:09:16.360 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
19:09:16.361 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
19:09:16.361 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
19:09:16.361 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
19:09:16.361 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:16.361 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
19:09:16.362 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
19:09:16.362 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
19:09:16.362 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
19:09:16.362 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:16.363 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
19:09:16.363 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
19:09:16.363 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:16.363 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
19:09:16.363 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
19:09:16.382 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
19:09:16.382 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
19:09:16.427 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
19:09:16.428 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
19:09:17.065 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
19:09:17.065 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:17.066 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:17.068 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
19:09:17.070 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:17.073 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:17.073 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:17.074 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:17.100 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:17.100 INFO  DataSourceUtils - 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	2025-05-19 19:09:17	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:17.101 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
19:09:17.139 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
19:09:17.139 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
19:09:17.140 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
19:09:17.148 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:17.148 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
19:09:17.148 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:17.149 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:17.149 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
19:09:17.226 INFO  Funcotator - Initializing Funcotator Engine...
19:09:17.226 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:09:17.226 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:17.226 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.44846052426522806615.vcf
19:09:17.227 INFO  ProgressMeter - Starting traversal
19:09:17.227 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:17.347 INFO  ProgressMeter -             unmapped              0.0                     4           2000.0
19:09:17.347 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
19:09:17.347 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:09:17.348 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2686451712
19:09:17.436 INFO  Funcotator - ------------------------------------------------------------
19:09:17.436 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:17.436 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:17.436 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:17.436 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:17.436 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:17 PM GMT
19:09:17.436 INFO  Funcotator - ------------------------------------------------------------
19:09:17.436 INFO  Funcotator - ------------------------------------------------------------
19:09:17.436 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:17.436 INFO  Funcotator - Picard Version: 3.4.0
19:09:17.436 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:17.436 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:17.436 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:17.436 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:17.436 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:17.436 INFO  Funcotator - Deflater: IntelDeflater
19:09:17.436 INFO  Funcotator - Inflater: IntelInflater
19:09:17.436 INFO  Funcotator - GCS max retries/reopens: 20
19:09:17.436 INFO  Funcotator - Requester pays: disabled
19:09:17.436 INFO  Funcotator - Initializing engine
19:09:17.437 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
19:09:17.438 INFO  Funcotator - Done initializing engine
19:09:17.438 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:17.438 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:17.438 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder17997482367077520614/TranscriptIdFile.txt
19:09:17.438 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
19:09:17.438 INFO  FuncotatorEngine - Transcript parsing complete.
19:09:17.438 INFO  Funcotator - Initializing data sources...
19:09:17.438 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:17.438 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:17.439 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
19:09:17.439 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
19:09:17.439 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
19:09:17.439 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
19:09:17.439 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
19:09:17.440 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
19:09:17.440 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
19:09:17.440 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:17.440 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
19:09:17.440 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
19:09:17.441 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
19:09:17.441 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
19:09:17.441 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:17.441 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
19:09:17.441 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
19:09:17.441 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:17.441 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
19:09:17.442 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
19:09:17.461 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
19:09:17.462 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
19:09:17.624 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
19:09:17.625 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
19:09:18.275 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
19:09:18.275 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:18.276 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:18.278 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:18.281 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:18.284 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:18.284 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:18.285 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:18.312 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:18.313 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-19 19:09:18	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:18.313 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
19:09:18.351 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
19:09:18.351 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
19:09:18.351 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
19:09:18.359 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:18.360 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
19:09:18.360 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:18.360 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:18.361 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
19:09:18.435 INFO  Funcotator - Initializing Funcotator Engine...
19:09:18.435 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
19:09:18.436 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
19:09:18.436 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
19:09:18.436 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
19:09:18.436 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
19:09:18.437 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
19:09:18.437 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:18.437 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.316967909003755742833.maf
19:09:18.439 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
19:09:18.441 INFO  ProgressMeter - Starting traversal
19:09:18.441 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:18.471 INFO  ProgressMeter -             unmapped              0.0                     3           6000.0
19:09:18.471 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
19:09:18.471 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:09:18.471 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:18 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2883584000
19:09:18.623 INFO  Funcotator - ------------------------------------------------------------
19:09:18.623 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:18.623 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:18.623 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:18.623 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:18.623 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:18 PM GMT
19:09:18.623 INFO  Funcotator - ------------------------------------------------------------
19:09:18.623 INFO  Funcotator - ------------------------------------------------------------
19:09:18.623 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:18.623 INFO  Funcotator - Picard Version: 3.4.0
19:09:18.623 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:18.623 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:18.623 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:18.623 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:18.623 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:18.623 INFO  Funcotator - Deflater: IntelDeflater
19:09:18.623 INFO  Funcotator - Inflater: IntelInflater
19:09:18.623 INFO  Funcotator - GCS max retries/reopens: 20
19:09:18.623 INFO  Funcotator - Requester pays: disabled
19:09:18.623 INFO  Funcotator - Initializing engine
19:09:18.624 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
19:09:18.625 INFO  Funcotator - Done initializing engine
19:09:18.625 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:18.625 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:18.625 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder9711412804940340014/TranscriptIdFile.txt
19:09:18.625 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
19:09:18.625 INFO  FuncotatorEngine - Transcript parsing complete.
19:09:18.625 INFO  Funcotator - Initializing data sources...
19:09:18.625 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:18.625 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:18.625 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
19:09:18.626 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
19:09:18.626 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
19:09:18.626 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
19:09:18.626 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
19:09:18.626 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
19:09:18.627 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:18.627 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:18.627 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
19:09:18.627 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
19:09:18.627 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
19:09:18.627 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
19:09:18.627 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:18.628 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
19:09:18.628 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
19:09:18.628 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:18.628 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
19:09:18.628 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
19:09:18.649 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
19:09:18.649 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
19:09:18.694 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
19:09:18.695 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
19:09:19.355 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
19:09:19.356 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:19.356 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:19.358 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
19:09:19.361 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:19.363 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:19.364 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:19.364 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:19.391 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:19.391 INFO  DataSourceUtils - 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	2025-05-19 19:09:19	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:19.391 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
19:09:19.429 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
19:09:19.429 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
19:09:19.430 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
19:09:19.437 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:19.438 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
19:09:19.438 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:19.439 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:19.439 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
19:09:19.514 INFO  Funcotator - Initializing Funcotator Engine...
19:09:19.514 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:09:19.514 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:19.514 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.49754858749664316783.maf
19:09:19.515 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
19:09:19.516 INFO  ProgressMeter - Starting traversal
19:09:19.516 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:19.639 INFO  ProgressMeter -             unmapped              0.0                     4           1951.2
19:09:19.639 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
19:09:19.639 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:09:19.639 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:19 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2986344448
19:09:19.774 INFO  Funcotator - ------------------------------------------------------------
19:09:19.774 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:19.774 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:19.774 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:19.774 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:19.774 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:19 PM GMT
19:09:19.774 INFO  Funcotator - ------------------------------------------------------------
19:09:19.774 INFO  Funcotator - ------------------------------------------------------------
19:09:19.774 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:19.774 INFO  Funcotator - Picard Version: 3.4.0
19:09:19.774 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:19.774 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:19.774 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:19.774 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:19.774 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:19.774 INFO  Funcotator - Deflater: IntelDeflater
19:09:19.774 INFO  Funcotator - Inflater: IntelInflater
19:09:19.774 INFO  Funcotator - GCS max retries/reopens: 20
19:09:19.774 INFO  Funcotator - Requester pays: disabled
19:09:19.774 INFO  Funcotator - Initializing engine
19:09:19.775 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
19:09:19.776 INFO  Funcotator - Done initializing engine
19:09:19.776 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:19.776 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:19.776 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder8248518950437943943/TranscriptIdFile.txt
19:09:19.776 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
19:09:19.776 INFO  FuncotatorEngine - Transcript parsing complete.
19:09:19.776 INFO  Funcotator - Initializing data sources...
19:09:19.776 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:19.776 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:19.776 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
19:09:19.777 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
19:09:19.777 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
19:09:19.777 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
19:09:19.777 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
19:09:19.777 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
19:09:19.777 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
19:09:19.778 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:19.778 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
19:09:19.778 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
19:09:19.778 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
19:09:19.778 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
19:09:19.779 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:19.779 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
19:09:19.779 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
19:09:19.779 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:19.779 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
19:09:19.779 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
19:09:19.798 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
19:09:19.799 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
19:09:19.845 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
19:09:19.845 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
19:09:20.467 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:20.467 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:20.468 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:20.470 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
19:09:20.472 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:20.474 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:20.475 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:20.475 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:20.502 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:20.502 INFO  DataSourceUtils - 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	2025-05-19 19:09:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:20.502 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
19:09:20.577 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
19:09:20.577 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
19:09:20.578 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
19:09:20.593 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:20.594 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
19:09:20.594 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:20.594 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:20.595 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
19:09:20.714 INFO  Funcotator - Initializing Funcotator Engine...
19:09:20.714 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
19:09:20.715 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
19:09:20.715 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
19:09:20.715 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
19:09:20.715 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
19:09:20.715 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:20.715 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.312892419424712497826.maf
19:09:20.716 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
19:09:20.717 INFO  ProgressMeter - Starting traversal
19:09:20.717 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:20.754 INFO  ProgressMeter -             unmapped              0.0                     3           4864.9
19:09:20.754 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
19:09:20.754 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:09:20.754 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:20 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3063939072
19:09:20.870 INFO  Funcotator - ------------------------------------------------------------
19:09:20.870 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:20.870 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:20.870 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:20.870 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:20.870 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:20 PM GMT
19:09:20.870 INFO  Funcotator - ------------------------------------------------------------
19:09:20.870 INFO  Funcotator - ------------------------------------------------------------
19:09:20.870 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:20.870 INFO  Funcotator - Picard Version: 3.4.0
19:09:20.870 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:20.870 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:20.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:20.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:20.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:20.870 INFO  Funcotator - Deflater: IntelDeflater
19:09:20.870 INFO  Funcotator - Inflater: IntelInflater
19:09:20.870 INFO  Funcotator - GCS max retries/reopens: 20
19:09:20.870 INFO  Funcotator - Requester pays: disabled
19:09:20.870 INFO  Funcotator - Initializing engine
19:09:20.871 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
19:09:20.872 INFO  Funcotator - Done initializing engine
19:09:20.872 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:20.872 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:20.872 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder9164645418928344575/TranscriptIdFile.txt
19:09:20.872 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
19:09:20.872 INFO  FuncotatorEngine - Transcript parsing complete.
19:09:20.872 INFO  Funcotator - Initializing data sources...
19:09:20.872 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:20.872 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:20.872 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
19:09:20.873 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
19:09:20.873 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
19:09:20.873 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
19:09:20.873 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
19:09:20.873 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
19:09:20.873 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
19:09:20.874 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:20.874 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
19:09:20.874 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
19:09:20.874 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
19:09:20.874 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
19:09:20.875 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:20.875 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
19:09:20.875 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
19:09:20.875 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:20.875 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
19:09:20.875 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
19:09:20.895 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
19:09:20.895 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
19:09:20.993 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
19:09:20.994 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
19:09:21.673 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
19:09:21.673 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:21.674 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:21.678 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
19:09:21.683 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:21.686 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:21.687 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:21.687 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:21.727 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:21.727 INFO  DataSourceUtils - 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	2025-05-19 19:09:21	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:21.728 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
19:09:21.767 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
19:09:21.767 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
19:09:21.768 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
19:09:21.775 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:21.776 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
19:09:21.776 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:21.777 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:21.778 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
19:09:21.855 INFO  Funcotator - Initializing Funcotator Engine...
19:09:21.855 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:09:21.855 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:21.855 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.49581076476244399389.maf
19:09:21.855 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
19:09:21.857 INFO  ProgressMeter - Starting traversal
19:09:21.857 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:21.972 INFO  ProgressMeter -             unmapped              0.0                     4           2087.0
19:09:21.972 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
19:09:21.972 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:09:21.972 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:21 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3145728000
19:09:22.056 INFO  Funcotator - ------------------------------------------------------------
19:09:22.056 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:22.056 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:22.056 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:22.056 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:22.056 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:22 PM GMT
19:09:22.056 INFO  Funcotator - ------------------------------------------------------------
19:09:22.056 INFO  Funcotator - ------------------------------------------------------------
19:09:22.056 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:22.056 INFO  Funcotator - Picard Version: 3.4.0
19:09:22.056 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:22.056 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:22.057 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:22.057 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:22.057 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:22.057 INFO  Funcotator - Deflater: IntelDeflater
19:09:22.057 INFO  Funcotator - Inflater: IntelInflater
19:09:22.057 INFO  Funcotator - GCS max retries/reopens: 20
19:09:22.057 INFO  Funcotator - Requester pays: disabled
19:09:22.057 INFO  Funcotator - Initializing engine
19:09:22.059 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
19:09:22.060 INFO  Funcotator - Done initializing engine
19:09:22.060 INFO  Funcotator - Validating sequence dictionaries...
19:09:22.060 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:22.061 INFO  Funcotator - Initializing data sources...
19:09:22.061 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:22.061 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:22.061 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
19:09:22.061 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
19:09:22.061 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
19:09:22.062 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
19:09:22.062 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
19:09:22.062 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
19:09:22.062 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
19:09:22.062 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:22.062 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
19:09:22.063 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
19:09:22.063 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
19:09:22.063 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
19:09:22.063 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:22.064 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
19:09:22.064 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
19:09:22.064 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:22.064 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
19:09:22.064 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
19:09:22.083 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
19:09:22.084 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
19:09:22.130 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
19:09:22.131 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
19:09:22.786 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
19:09:22.786 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:22.787 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:22.789 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
19:09:22.792 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:22.794 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:22.794 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:22.795 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:22.821 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:22.821 INFO  DataSourceUtils - 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	2025-05-19 19:09:22	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:22.822 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
19:09:22.860 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
19:09:22.860 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
19:09:22.860 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
19:09:22.868 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:22.869 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
19:09:22.869 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:22.870 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:22.870 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
19:09:22.945 INFO  Funcotator - Initializing Funcotator Engine...
19:09:22.945 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:22.945 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.
19:09:22.945 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator8665233827629277489.vcf
19:09:22.947 INFO  ProgressMeter - Starting traversal
19:09:22.947 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:25.182 INFO  ProgressMeter -             unmapped              0.0                   198           5315.4
19:09:25.182 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
19:09:25.182 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
19:09:25.191 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:25 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3145728000
19:09:25.193 WARN  gatk -   VCF Elapsed Time: 3.218049198s
19:09:25.194 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet1.vcf.funcotator8665233827629277489.vcf
19:09:25.198 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
19:09:25.311 INFO  Funcotator - ------------------------------------------------------------
19:09:25.311 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:25.311 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:25.311 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:25.311 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:25.311 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:25 PM GMT
19:09:25.311 INFO  Funcotator - ------------------------------------------------------------
19:09:25.311 INFO  Funcotator - ------------------------------------------------------------
19:09:25.311 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:25.311 INFO  Funcotator - Picard Version: 3.4.0
19:09:25.311 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:25.311 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:25.311 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:25.311 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:25.311 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:25.311 INFO  Funcotator - Deflater: IntelDeflater
19:09:25.311 INFO  Funcotator - Inflater: IntelInflater
19:09:25.311 INFO  Funcotator - GCS max retries/reopens: 20
19:09:25.311 INFO  Funcotator - Requester pays: disabled
19:09:25.311 INFO  Funcotator - Initializing engine
19:09:25.313 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
19:09:25.315 INFO  Funcotator - Done initializing engine
19:09:25.315 INFO  Funcotator - Validating sequence dictionaries...
19:09:25.315 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:25.315 INFO  Funcotator - Initializing data sources...
19:09:25.315 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:25.315 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:25.315 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
19:09:25.315 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
19:09:25.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
19:09:25.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
19:09:25.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
19:09:25.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
19:09:25.316 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
19:09:25.317 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:25.317 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
19:09:25.317 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
19:09:25.317 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
19:09:25.317 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
19:09:25.317 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:25.318 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:25.318 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
19:09:25.318 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:25.318 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
19:09:25.318 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
19:09:25.345 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
19:09:25.346 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
19:09:25.391 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
19:09:25.391 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
19:09:25.960 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:25.960 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:25.962 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:25.965 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
19:09:25.969 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:25.971 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:25.971 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:25.972 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:25.998 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:25.998 INFO  DataSourceUtils - 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	2025-05-19 19:09:25	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:25.999 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
19:09:26.036 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
19:09:26.036 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
19:09:26.036 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
19:09:26.044 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:26.045 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
19:09:26.045 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:26.045 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:26.046 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
19:09:26.120 INFO  Funcotator - Initializing Funcotator Engine...
19:09:26.120 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:26.120 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
19:09:26.120 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator13672741873578297292.maf
19:09:26.121 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
19:09:26.122 INFO  ProgressMeter - Starting traversal
19:09:26.122 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:28.165 INFO  ProgressMeter -             unmapped              0.0                   198           5815.0
19:09:28.165 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
19:09:28.165 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
19:09:28.166 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:28 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3145728000
19:09:28.166 WARN  gatk -   MAF Elapsed Time: 2.962576412s
19:09:28.255 INFO  Funcotator - ------------------------------------------------------------
19:09:28.255 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:28.255 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:28.255 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:28.255 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:28.255 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:28 PM GMT
19:09:28.255 INFO  Funcotator - ------------------------------------------------------------
19:09:28.255 INFO  Funcotator - ------------------------------------------------------------
19:09:28.255 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:28.255 INFO  Funcotator - Picard Version: 3.4.0
19:09:28.255 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:28.255 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:28.255 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:28.255 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:28.255 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:28.255 INFO  Funcotator - Deflater: IntelDeflater
19:09:28.255 INFO  Funcotator - Inflater: IntelInflater
19:09:28.255 INFO  Funcotator - GCS max retries/reopens: 20
19:09:28.256 INFO  Funcotator - Requester pays: disabled
19:09:28.256 INFO  Funcotator - Initializing engine
19:09:28.258 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
19:09:28.259 INFO  Funcotator - Done initializing engine
19:09:28.259 INFO  Funcotator - Validating sequence dictionaries...
19:09:28.259 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:28.259 INFO  Funcotator - Initializing data sources...
19:09:28.259 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:28.259 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:28.260 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
19:09:28.260 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
19:09:28.260 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
19:09:28.260 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
19:09:28.261 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
19:09:28.261 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
19:09:28.261 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
19:09:28.261 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:28.261 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
19:09:28.261 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
19:09:28.262 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
19:09:28.262 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
19:09:28.262 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:28.262 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
19:09:28.262 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
19:09:28.262 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:28.262 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
19:09:28.263 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
19:09:28.282 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
19:09:28.283 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
19:09:28.329 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
19:09:28.330 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
19:09:28.900 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
19:09:28.900 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:28.901 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:28.903 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
19:09:28.906 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:28.908 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:28.908 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:28.909 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:28.939 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:28.939 INFO  DataSourceUtils - 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	2025-05-19 19:09:28	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:28.939 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
19:09:28.977 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
19:09:28.977 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
19:09:28.978 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
19:09:28.986 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:28.986 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
19:09:28.986 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:28.987 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:28.987 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
19:09:29.063 INFO  Funcotator - Initializing Funcotator Engine...
19:09:29.063 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:29.063 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.
19:09:29.063 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator5202086825818423284.vcf
19:09:29.065 INFO  ProgressMeter - Starting traversal
19:09:29.065 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:30.133 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
19:09:30.133 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
19:09:30.919 INFO  ProgressMeter -             unmapped              0.0                   168           5436.9
19:09:30.920 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
19:09:30.920 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
19:09:30.926 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:30 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=3145728000
19:09:30.926 WARN  gatk -   VCF Elapsed Time: 2.757904807s
19:09:30.927 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet2.vcf.funcotator5202086825818423284.vcf
19:09:30.929 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf
19:09:31.019 INFO  Funcotator - ------------------------------------------------------------
19:09:31.019 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:31.019 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:31.020 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:31.020 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:31.020 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:31 PM GMT
19:09:31.020 INFO  Funcotator - ------------------------------------------------------------
19:09:31.020 INFO  Funcotator - ------------------------------------------------------------
19:09:31.020 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:31.020 INFO  Funcotator - Picard Version: 3.4.0
19:09:31.020 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:31.020 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:31.020 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:31.020 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:31.020 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:31.020 INFO  Funcotator - Deflater: IntelDeflater
19:09:31.020 INFO  Funcotator - Inflater: IntelInflater
19:09:31.020 INFO  Funcotator - GCS max retries/reopens: 20
19:09:31.020 INFO  Funcotator - Requester pays: disabled
19:09:31.020 INFO  Funcotator - Initializing engine
19:09:31.023 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
19:09:31.024 INFO  Funcotator - Done initializing engine
19:09:31.024 INFO  Funcotator - Validating sequence dictionaries...
19:09:31.025 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:31.025 INFO  Funcotator - Initializing data sources...
19:09:31.025 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:31.025 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:31.025 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
19:09:31.025 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
19:09:31.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
19:09:31.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
19:09:31.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
19:09:31.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
19:09:31.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:31.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:31.027 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
19:09:31.027 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
19:09:31.027 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
19:09:31.027 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
19:09:31.027 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:31.028 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:31.028 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
19:09:31.028 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:31.028 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
19:09:31.028 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
19:09:31.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
19:09:31.059 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
19:09:31.110 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
19:09:31.111 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
19:09:31.681 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:31.681 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:31.682 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:31.685 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
19:09:31.687 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:31.690 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:31.690 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:31.690 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:31.717 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:31.717 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-19 19:09:31	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:31.717 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
19:09:31.755 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
19:09:31.756 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
19:09:31.756 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
19:09:31.764 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:31.764 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
19:09:31.764 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:31.765 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:31.765 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
19:09:31.839 INFO  Funcotator - Initializing Funcotator Engine...
19:09:31.840 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:31.840 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.
19:09:31.840 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator14969750396511606096.maf
19:09:31.840 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
19:09:31.841 INFO  ProgressMeter - Starting traversal
19:09:31.842 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:32.875 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
19:09:32.876 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
19:09:33.636 INFO  ProgressMeter -             unmapped              0.0                   168           5618.7
19:09:33.636 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
19:09:33.636 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
19:09:33.637 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:33 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=3145728000
19:09:33.637 WARN  gatk -   MAF Elapsed Time: 2.702913583s
19:09:33.721 INFO  Funcotator - ------------------------------------------------------------
19:09:33.721 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:33.721 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:33.721 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:33.721 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:33.721 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:33 PM GMT
19:09:33.721 INFO  Funcotator - ------------------------------------------------------------
19:09:33.721 INFO  Funcotator - ------------------------------------------------------------
19:09:33.721 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:33.721 INFO  Funcotator - Picard Version: 3.4.0
19:09:33.721 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:33.721 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:33.721 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:33.721 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:33.721 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:33.721 INFO  Funcotator - Deflater: IntelDeflater
19:09:33.722 INFO  Funcotator - Inflater: IntelInflater
19:09:33.722 INFO  Funcotator - GCS max retries/reopens: 20
19:09:33.722 INFO  Funcotator - Requester pays: disabled
19:09:33.722 INFO  Funcotator - Initializing engine
19:09:33.724 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
19:09:33.725 INFO  Funcotator - Done initializing engine
19:09:33.725 INFO  Funcotator - Validating sequence dictionaries...
19:09:33.725 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:33.725 INFO  Funcotator - Initializing data sources...
19:09:33.725 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:33.725 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:33.726 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
19:09:33.726 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
19:09:33.726 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
19:09:33.726 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
19:09:33.726 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
19:09:33.727 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
19:09:33.727 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:33.727 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:33.727 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
19:09:33.743 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
19:09:33.743 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
19:09:33.743 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
19:09:33.743 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:33.743 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
19:09:33.743 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
19:09:33.743 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:33.743 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
19:09:33.744 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
19:09:33.764 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
19:09:33.765 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
19:09:33.809 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
19:09:33.810 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
19:09:34.404 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:34.404 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:34.405 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:34.407 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
19:09:34.410 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:34.412 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:34.412 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:34.412 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:34.439 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:34.439 INFO  DataSourceUtils - 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	2025-05-19 19:09:34	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:34.439 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
19:09:34.477 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
19:09:34.477 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
19:09:34.478 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
19:09:34.486 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:34.486 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
19:09:34.486 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:34.487 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:34.487 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
19:09:34.563 INFO  Funcotator - Initializing Funcotator Engine...
19:09:34.563 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:34.563 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.
19:09:34.563 INFO  Funcotator - Creating a VCF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator10264689550016340394.vcf
19:09:34.564 INFO  ProgressMeter - Starting traversal
19:09:34.564 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:34.574 INFO  ProgressMeter -             unmapped              0.0                     1           6000.0
19:09:34.574 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
19:09:34.575 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:09:34.576 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:34 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3145728000
19:09:34.576 WARN  gatk -   VCF Elapsed Time: 0.937197738s
19:09:34.576 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/hashSetOrderingIssue.vcf.funcotator10264689550016340394.vcf
19:09:34.578 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf
19:09:34.664 INFO  Funcotator - ------------------------------------------------------------
19:09:34.664 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:34.664 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:34.664 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:34.664 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:34.664 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:34 PM GMT
19:09:34.664 INFO  Funcotator - ------------------------------------------------------------
19:09:34.664 INFO  Funcotator - ------------------------------------------------------------
19:09:34.664 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:34.664 INFO  Funcotator - Picard Version: 3.4.0
19:09:34.664 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:34.664 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:34.664 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:34.664 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:34.664 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:34.664 INFO  Funcotator - Deflater: IntelDeflater
19:09:34.664 INFO  Funcotator - Inflater: IntelInflater
19:09:34.664 INFO  Funcotator - GCS max retries/reopens: 20
19:09:34.664 INFO  Funcotator - Requester pays: disabled
19:09:34.664 INFO  Funcotator - Initializing engine
19:09:34.666 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
19:09:34.667 INFO  Funcotator - Done initializing engine
19:09:34.667 INFO  Funcotator - Validating sequence dictionaries...
19:09:34.668 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:34.668 INFO  Funcotator - Initializing data sources...
19:09:34.668 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:34.668 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:34.668 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
19:09:34.668 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
19:09:34.668 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
19:09:34.669 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
19:09:34.669 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
19:09:34.669 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
19:09:34.669 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
19:09:34.669 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:34.669 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
19:09:34.670 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
19:09:34.670 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
19:09:34.670 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
19:09:34.670 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:34.670 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
19:09:34.670 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
19:09:34.670 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:34.670 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
19:09:34.671 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
19:09:34.690 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
19:09:34.691 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
19:09:34.787 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
19:09:34.787 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
19:09:35.394 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
19:09:35.394 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:35.395 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:35.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:35.400 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:35.402 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:35.403 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
19:09:35.403 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:35.431 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:35.431 INFO  DataSourceUtils - 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	2025-05-19 19:09:35	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:35.431 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
19:09:35.469 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
19:09:35.469 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
19:09:35.470 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
19:09:35.480 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:35.481 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
19:09:35.481 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:35.482 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:35.482 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
19:09:35.601 INFO  Funcotator - Initializing Funcotator Engine...
19:09:35.601 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:35.601 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.
19:09:35.602 INFO  Funcotator - Creating a MAF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator14816125587425624460.maf
19:09:35.602 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
19:09:35.603 INFO  ProgressMeter - Starting traversal
19:09:35.603 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:35.619 INFO  ProgressMeter -             unmapped              0.0                     1           3750.0
19:09:35.619 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
19:09:35.619 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:09:35.620 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:35 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3206545408
19:09:35.620 WARN  gatk -   MAF Elapsed Time: 1.041295704s
19:09:35.721 INFO  Funcotator - ------------------------------------------------------------
19:09:35.721 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:35.721 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:35.721 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:35.721 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:35.721 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:35 PM GMT
19:09:35.721 INFO  Funcotator - ------------------------------------------------------------
19:09:35.721 INFO  Funcotator - ------------------------------------------------------------
19:09:35.721 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:35.721 INFO  Funcotator - Picard Version: 3.4.0
19:09:35.721 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:35.721 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:35.721 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:35.721 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:35.721 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:35.721 INFO  Funcotator - Deflater: IntelDeflater
19:09:35.721 INFO  Funcotator - Inflater: IntelInflater
19:09:35.721 INFO  Funcotator - GCS max retries/reopens: 20
19:09:35.721 INFO  Funcotator - Requester pays: disabled
19:09:35.721 INFO  Funcotator - Initializing engine
19:09:35.746 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
19:09:35.769 INFO  Funcotator - Done initializing engine
19:09:35.769 INFO  Funcotator - Validating sequence dictionaries...
19:09:35.776 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:35.776 INFO  Funcotator - Initializing data sources...
19:09:35.776 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:35.776 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:35.776 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
19:09:35.777 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
19:09:35.777 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
19:09:35.777 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
19:09:35.777 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
19:09:35.777 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
19:09:35.777 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
19:09:35.778 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
19:09:35.778 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
19:09:35.778 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
19:09:35.778 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
19:09:35.779 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
19:09:35.779 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
19:09:35.779 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:35.779 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
19:09:35.779 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
19:09:35.798 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
19:09:35.799 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
19:09:35.886 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
19:09:35.886 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
19:09:36.528 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
19:09:36.528 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:36.529 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
19:09:36.530 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
19:09:36.532 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
19:09:36.534 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
19:09:36.611 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
19:09:36.611 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
19:09:36.611 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
19:09:36.619 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
19:09:36.619 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:36.620 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
19:09:36.620 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
19:09:36.621 INFO  Funcotator - Initializing Funcotator Engine...
19:09:36.625 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:36.625 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator12871419912542229700.vcf
19:09:36.636 INFO  ProgressMeter - Starting traversal
19:09:36.636 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:36.661 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.
19:09:36.663 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
19:09:36.666 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
19:09:36.669 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
19:09:36.669 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
19:09:36.669 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
19:09:36.669 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
19:09:36.669 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
19:09:36.670 INFO  ProgressMeter -             unmapped              0.0                     5           8823.5
19:09:36.670 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
19:09:36.670 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:09:36.681 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:36 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3298820096
19:09:36.682 WARN  gatk -   VCF Elapsed Time: 1.060928901s
19:09:36.682 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSetHG38.vcf.funcotator12871419912542229700.vcf
19:09:36.693 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf
19:09:36.786 INFO  Funcotator - ------------------------------------------------------------
19:09:36.786 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:36.786 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:36.786 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:36.786 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:36.786 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:36 PM GMT
19:09:36.786 INFO  Funcotator - ------------------------------------------------------------
19:09:36.786 INFO  Funcotator - ------------------------------------------------------------
19:09:36.787 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:36.787 INFO  Funcotator - Picard Version: 3.4.0
19:09:36.787 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:36.787 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:36.787 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:36.787 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:36.787 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:36.787 INFO  Funcotator - Deflater: IntelDeflater
19:09:36.787 INFO  Funcotator - Inflater: IntelInflater
19:09:36.787 INFO  Funcotator - GCS max retries/reopens: 20
19:09:36.787 INFO  Funcotator - Requester pays: disabled
19:09:36.787 INFO  Funcotator - Initializing engine
19:09:36.831 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
19:09:36.852 INFO  Funcotator - Done initializing engine
19:09:36.852 INFO  Funcotator - Validating sequence dictionaries...
19:09:36.859 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:36.859 INFO  Funcotator - Initializing data sources...
19:09:36.859 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:36.859 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:36.860 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
19:09:36.860 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
19:09:36.860 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
19:09:36.860 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
19:09:36.860 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
19:09:36.860 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
19:09:36.861 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
19:09:36.861 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
19:09:36.861 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
19:09:36.861 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
19:09:36.861 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
19:09:36.862 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
19:09:36.862 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
19:09:36.862 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:36.862 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
19:09:36.862 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
19:09:36.881 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
19:09:36.882 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
19:09:36.927 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
19:09:36.927 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
19:09:37.624 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
19:09:37.624 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:37.625 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
19:09:37.627 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
19:09:37.629 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
19:09:37.630 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
19:09:37.694 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
19:09:37.694 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
19:09:37.694 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg38/cosmic_tissue.tsv
19:09:37.702 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
19:09:37.702 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:37.703 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
19:09:37.704 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
19:09:37.705 INFO  Funcotator - Initializing Funcotator Engine...
19:09:37.708 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:37.708 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator17852183075725493466.maf
19:09:37.710 INFO  ProgressMeter - Starting traversal
19:09:37.710 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:37.732 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.
19:09:37.732 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
19:09:37.734 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
19:09:37.737 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
19:09:37.738 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
19:09:37.738 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
19:09:37.738 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
19:09:37.738 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
19:09:37.739 INFO  ProgressMeter -             unmapped              0.0                     5          10344.8
19:09:37.739 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
19:09:37.739 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:09:37.739 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:37 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2845835264
19:09:37.739 WARN  gatk -   MAF Elapsed Time: 1.038684797s
19:09:37.826 INFO  Funcotator - ------------------------------------------------------------
19:09:37.826 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:37.826 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:37.826 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:37.826 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:37.826 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:37 PM GMT
19:09:37.826 INFO  Funcotator - ------------------------------------------------------------
19:09:37.826 INFO  Funcotator - ------------------------------------------------------------
19:09:37.826 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:37.826 INFO  Funcotator - Picard Version: 3.4.0
19:09:37.826 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:37.826 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:37.826 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:37.826 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:37.826 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:37.826 INFO  Funcotator - Deflater: IntelDeflater
19:09:37.826 INFO  Funcotator - Inflater: IntelInflater
19:09:37.826 INFO  Funcotator - GCS max retries/reopens: 20
19:09:37.826 INFO  Funcotator - Requester pays: disabled
19:09:37.826 INFO  Funcotator - Initializing engine
19:09:37.828 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
19:09:37.830 INFO  Funcotator - Done initializing engine
19:09:37.830 INFO  Funcotator - Validating sequence dictionaries...
19:09:37.830 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:37.830 INFO  Funcotator - Initializing data sources...
19:09:37.830 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:37.830 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:37.831 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
19:09:37.831 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
19:09:37.831 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
19:09:37.831 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
19:09:37.831 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
19:09:37.831 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
19:09:37.832 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
19:09:37.832 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:37.832 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
19:09:37.832 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
19:09:37.832 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
19:09:37.833 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
19:09:37.833 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:37.833 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
19:09:37.833 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
19:09:37.833 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:37.833 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
19:09:37.834 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
19:09:37.852 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
19:09:37.853 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
19:09:37.898 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
19:09:37.899 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
19:09:38.530 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
19:09:38.530 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:38.531 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:38.533 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
19:09:38.536 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:38.538 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:38.539 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:38.539 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:38.566 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:38.566 INFO  DataSourceUtils - 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	2025-05-19 19:09:38	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:38.567 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
19:09:38.606 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
19:09:38.606 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
19:09:38.606 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
19:09:38.614 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:38.615 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
19:09:38.615 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:38.615 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:38.616 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
19:09:38.698 INFO  Funcotator - Initializing Funcotator Engine...
19:09:38.698 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:38.698 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.
19:09:38.698 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator3756950076778443626.vcf
19:09:38.701 INFO  ProgressMeter - Starting traversal
19:09:38.701 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:44.261 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
19:09:44.262 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
19:09:44.263 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          16256.7
19:09:44.263 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
19:09:44.263 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
19:09:44.286 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:44 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3177185280
19:09:44.286 WARN  gatk -   VCF Elapsed Time: 6.544976141s
19:09:44.286 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestHg19Large.vcf.funcotator3756950076778443626.vcf
19:09:44.295 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf
19:09:44.403 INFO  Funcotator - ------------------------------------------------------------
19:09:44.403 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:44.403 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:44.403 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:44.403 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:44.403 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:44 PM GMT
19:09:44.403 INFO  Funcotator - ------------------------------------------------------------
19:09:44.403 INFO  Funcotator - ------------------------------------------------------------
19:09:44.403 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:44.403 INFO  Funcotator - Picard Version: 3.4.0
19:09:44.403 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:44.403 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:44.403 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:44.403 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:44.403 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:44.403 INFO  Funcotator - Deflater: IntelDeflater
19:09:44.403 INFO  Funcotator - Inflater: IntelInflater
19:09:44.403 INFO  Funcotator - GCS max retries/reopens: 20
19:09:44.403 INFO  Funcotator - Requester pays: disabled
19:09:44.403 INFO  Funcotator - Initializing engine
19:09:44.405 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
19:09:44.406 INFO  Funcotator - Done initializing engine
19:09:44.406 INFO  Funcotator - Validating sequence dictionaries...
19:09:44.407 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:44.407 INFO  Funcotator - Initializing data sources...
19:09:44.407 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:44.407 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:44.407 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
19:09:44.407 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
19:09:44.407 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
19:09:44.407 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
19:09:44.408 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
19:09:44.408 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
19:09:44.408 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
19:09:44.408 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:44.408 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
19:09:44.409 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
19:09:44.409 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
19:09:44.409 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
19:09:44.409 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:44.409 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
19:09:44.409 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
19:09:44.409 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:44.409 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
19:09:44.410 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
19:09:44.435 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
19:09:44.435 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
19:09:44.481 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
19:09:44.481 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
19:09:45.016 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:45.016 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:45.017 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:45.019 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
19:09:45.021 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:45.023 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:45.023 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:45.024 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:45.050 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:45.050 INFO  DataSourceUtils - 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	2025-05-19 19:09:45	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:45.051 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
19:09:45.158 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
19:09:45.158 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
19:09:45.158 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
19:09:45.165 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:45.166 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
19:09:45.166 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:45.167 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:45.167 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
19:09:45.241 INFO  Funcotator - Initializing Funcotator Engine...
19:09:45.241 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:45.241 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.
19:09:45.241 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator17093511027720131736.maf
19:09:45.242 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
19:09:45.242 INFO  ProgressMeter - Starting traversal
19:09:45.242 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:50.353 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
19:09:50.354 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
19:09:50.354 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          17687.8
19:09:50.354 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
19:09:50.354 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
19:09:50.355 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:50 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3177185280
19:09:50.355 WARN  gatk -   MAF Elapsed Time: 6.038072266s
19:09:50.458 INFO  Funcotator - ------------------------------------------------------------
19:09:50.458 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:50.458 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:50.458 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:50.458 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:50.458 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:50 PM GMT
19:09:50.459 INFO  Funcotator - ------------------------------------------------------------
19:09:50.459 INFO  Funcotator - ------------------------------------------------------------
19:09:50.459 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:50.459 INFO  Funcotator - Picard Version: 3.4.0
19:09:50.459 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:50.459 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:50.459 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:50.459 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:50.459 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:50.459 INFO  Funcotator - Deflater: IntelDeflater
19:09:50.459 INFO  Funcotator - Inflater: IntelInflater
19:09:50.459 INFO  Funcotator - GCS max retries/reopens: 20
19:09:50.459 INFO  Funcotator - Requester pays: disabled
19:09:50.459 INFO  Funcotator - Initializing engine
19:09:50.461 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
19:09:50.462 INFO  Funcotator - Done initializing engine
19:09:50.462 INFO  Funcotator - Validating sequence dictionaries...
19:09:50.462 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:50.462 INFO  Funcotator - Initializing data sources...
19:09:50.462 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:50.462 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:50.463 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
19:09:50.463 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
19:09:50.463 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
19:09:50.463 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
19:09:50.463 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
19:09:50.464 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
19:09:50.464 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
19:09:50.464 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:50.464 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
19:09:50.464 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
19:09:50.465 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
19:09:50.465 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
19:09:50.465 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:50.465 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
19:09:50.465 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
19:09:50.465 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:50.465 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
19:09:50.466 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
19:09:50.484 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
19:09:50.485 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
19:09:50.564 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
19:09:50.565 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
19:09:51.100 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
19:09:51.100 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:51.101 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:51.103 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
19:09:51.106 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:51.108 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:51.108 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
19:09:51.109 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:51.140 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
19:09:51.140 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
WARNING	2025-05-19 19:09:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:51.140 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
19:09:51.178 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
19:09:51.178 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
19:09:51.179 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
19:09:51.187 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:51.187 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
19:09:51.187 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:51.188 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:51.188 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
19:09:51.263 INFO  Funcotator - Initializing Funcotator Engine...
19:09:51.263 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:51.263 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.
19:09:51.264 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator15256153204009289633.vcf
19:09:51.265 INFO  ProgressMeter - Starting traversal
19:09:51.265 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:53.262 INFO  ProgressMeter -             unmapped              0.0                   198           5948.9
19:09:53.262 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
19:09:53.262 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
19:09:53.271 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:53 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3177185280
19:09:53.359 INFO  Funcotator - ------------------------------------------------------------
19:09:53.359 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:53.359 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:53.359 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:53.359 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:53.359 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:53 PM GMT
19:09:53.359 INFO  Funcotator - ------------------------------------------------------------
19:09:53.359 INFO  Funcotator - ------------------------------------------------------------
19:09:53.359 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:53.359 INFO  Funcotator - Picard Version: 3.4.0
19:09:53.359 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:53.359 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:53.359 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:53.359 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:53.359 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:53.359 INFO  Funcotator - Deflater: IntelDeflater
19:09:53.359 INFO  Funcotator - Inflater: IntelInflater
19:09:53.359 INFO  Funcotator - GCS max retries/reopens: 20
19:09:53.359 INFO  Funcotator - Requester pays: disabled
19:09:53.359 INFO  Funcotator - Initializing engine
19:09:53.362 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
19:09:53.363 INFO  Funcotator - Done initializing engine
19:09:53.363 INFO  Funcotator - Validating sequence dictionaries...
19:09:53.363 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:53.363 INFO  Funcotator - Initializing data sources...
19:09:53.363 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:53.363 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:53.363 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
19:09:53.364 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
19:09:53.364 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
19:09:53.364 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
19:09:53.364 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
19:09:53.364 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
19:09:53.364 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
19:09:53.365 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:53.365 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
19:09:53.365 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
19:09:53.365 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
19:09:53.365 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
19:09:53.365 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:53.365 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
19:09:53.365 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
19:09:53.365 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:53.366 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
19:09:53.366 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
19:09:53.385 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
19:09:53.385 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
19:09:53.463 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
19:09:53.464 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
19:09:53.999 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
19:09:53.999 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:54.000 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:54.002 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
19:09:54.004 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:54.006 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:54.006 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:54.007 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:54.033 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:54.033 INFO  DataSourceUtils - 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	2025-05-19 19:09:54	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:54.034 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
19:09:54.131 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
19:09:54.131 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
19:09:54.132 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
19:09:54.140 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:54.140 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
19:09:54.140 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:54.141 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:54.142 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
19:09:54.220 INFO  Funcotator - Initializing Funcotator Engine...
19:09:54.220 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:54.220 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.
19:09:54.220 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator7984032370495681044.maf
19:09:54.220 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
19:09:54.221 INFO  ProgressMeter - Starting traversal
19:09:54.221 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:56.164 INFO  ProgressMeter -             unmapped              0.0                   198           6114.3
19:09:56.164 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
19:09:56.164 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
19:09:56.164 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:56 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3177185280
19:09:56.264 INFO  Funcotator - ------------------------------------------------------------
19:09:56.264 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:56.264 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:56.264 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:56.264 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:56.264 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:56 PM GMT
19:09:56.264 INFO  Funcotator - ------------------------------------------------------------
19:09:56.264 INFO  Funcotator - ------------------------------------------------------------
19:09:56.264 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:56.264 INFO  Funcotator - Picard Version: 3.4.0
19:09:56.264 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:56.264 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:56.264 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:56.264 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:56.264 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:56.265 INFO  Funcotator - Deflater: IntelDeflater
19:09:56.265 INFO  Funcotator - Inflater: IntelInflater
19:09:56.265 INFO  Funcotator - GCS max retries/reopens: 20
19:09:56.265 INFO  Funcotator - Requester pays: disabled
19:09:56.265 INFO  Funcotator - Initializing engine
19:09:56.267 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
19:09:56.268 INFO  Funcotator - Done initializing engine
19:09:56.268 INFO  Funcotator - Validating sequence dictionaries...
19:09:56.268 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:56.268 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:56 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
19:09:56.354 INFO  Funcotator - ------------------------------------------------------------
19:09:56.354 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:56.354 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:56.354 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:56.354 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:56.354 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:56 PM GMT
19:09:56.354 INFO  Funcotator - ------------------------------------------------------------
19:09:56.354 INFO  Funcotator - ------------------------------------------------------------
19:09:56.354 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:56.354 INFO  Funcotator - Picard Version: 3.4.0
19:09:56.354 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:56.354 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:56.354 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:56.354 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:56.354 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:56.354 INFO  Funcotator - Deflater: IntelDeflater
19:09:56.354 INFO  Funcotator - Inflater: IntelInflater
19:09:56.355 INFO  Funcotator - GCS max retries/reopens: 20
19:09:56.355 INFO  Funcotator - Requester pays: disabled
19:09:56.355 INFO  Funcotator - Initializing engine
19:09:56.356 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
19:09:56.376 INFO  Funcotator - Done initializing engine
19:09:56.376 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:56.376 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:56.376 INFO  Funcotator - Initializing data sources...
19:09:56.376 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:09:56.376 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:56.376 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
19:09:56.376 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
19:09:56.376 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
19:09:56.376 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:56.376 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
19:09:56.376 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:56.377 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
19:09:56.377 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
19:09:56.378 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
19:09:56.378 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:09:56.378 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
19:09:56.387 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
19:09:56.396 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
19:09:56.405 INFO  Funcotator - Initializing Funcotator Engine...
19:09:56.409 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:56.409 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out15739837898748510537.vcf
19:09:56.421 INFO  ProgressMeter - Starting traversal
19:09:56.421 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:56.451 INFO  ProgressMeter -             unmapped              0.0                   100         200000.0
19:09:56.451 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
19:09:56.451 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
19:09:56.457 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:56 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
19:09:56.458 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out15739837898748510537.vcf
19:09:56.566 INFO  Funcotator - ------------------------------------------------------------
19:09:56.567 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:56.567 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:56.567 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:56.567 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:56.567 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:56 PM GMT
19:09:56.567 INFO  Funcotator - ------------------------------------------------------------
19:09:56.567 INFO  Funcotator - ------------------------------------------------------------
19:09:56.567 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:56.567 INFO  Funcotator - Picard Version: 3.4.0
19:09:56.567 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:56.567 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:56.567 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:56.567 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:56.567 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:56.567 INFO  Funcotator - Deflater: IntelDeflater
19:09:56.567 INFO  Funcotator - Inflater: IntelInflater
19:09:56.567 INFO  Funcotator - GCS max retries/reopens: 20
19:09:56.567 INFO  Funcotator - Requester pays: disabled
19:09:56.567 INFO  Funcotator - Initializing engine
19:09:56.568 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
19:09:56.570 INFO  Funcotator - Done initializing engine
19:09:56.570 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:56.570 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:56.570 INFO  Funcotator - Initializing data sources...
19:09:56.570 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:09:56.570 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:56.570 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
19:09:56.570 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
19:09:56.570 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
19:09:56.570 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:56.570 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
19:09:56.570 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:56.571 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
19:09:56.571 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
19:09:56.572 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
19:09:56.572 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:09:56.572 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
19:09:56.573 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
19:09:56.574 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
19:09:56.575 INFO  Funcotator - Initializing Funcotator Engine...
19:09:56.575 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:09:56.575 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.
19:09:56.575 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12647539419315877762.vcf
19:09:56.578 INFO  ProgressMeter - Starting traversal
19:09:56.578 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:56.587 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
19:09:56.587 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
19:09:56.587 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
19:09:56.589 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:56 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
19:09:56.590 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out12647539419315877762.vcf
19:09:56.677 INFO  Funcotator - ------------------------------------------------------------
19:09:56.677 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:56.677 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:56.677 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:56.677 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:56.677 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:56 PM GMT
19:09:56.677 INFO  Funcotator - ------------------------------------------------------------
19:09:56.677 INFO  Funcotator - ------------------------------------------------------------
19:09:56.677 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:56.677 INFO  Funcotator - Picard Version: 3.4.0
19:09:56.677 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:56.677 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:56.677 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:56.677 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:56.677 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:56.677 INFO  Funcotator - Deflater: IntelDeflater
19:09:56.677 INFO  Funcotator - Inflater: IntelInflater
19:09:56.677 INFO  Funcotator - GCS max retries/reopens: 20
19:09:56.677 INFO  Funcotator - Requester pays: disabled
19:09:56.677 INFO  Funcotator - Initializing engine
19:09:56.678 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
19:09:56.691 INFO  Funcotator - Done initializing engine
19:09:56.691 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:56.691 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:56.691 INFO  Funcotator - Initializing data sources...
19:09:56.691 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:09:56.691 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:56.691 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
19:09:56.691 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
19:09:56.691 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
19:09:56.691 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:56.691 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
19:09:56.691 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:56.692 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
19:09:56.692 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
19:09:56.693 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
19:09:56.693 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:09:56.693 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
19:09:56.701 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
19:09:56.709 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
19:09:56.717 INFO  Funcotator - Initializing Funcotator Engine...
19:09:56.720 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:09:56.721 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3320232582740438150.vcf
19:09:56.731 INFO  ProgressMeter - Starting traversal
19:09:56.731 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:56.735 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)
19:09:56.736 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)
19:09:56.736 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:09:56.736 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
19:09:56.736 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
19:09:56.736 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
19:09:56.738 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:09:56.739 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
19:09:56.739 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
19:09:56.739 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
19:09:56.739 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)
19:09:56.740 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)
19:09:56.740 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:09:56.740 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
19:09:56.740 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
19:09:56.740 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
19:09:56.740 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)
19:09:56.741 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)
19:09:56.741 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
19:09:56.741 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
19:09:56.741 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
19:09:56.741 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
19:09:56.742 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:09:56.742 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
19:09:56.742 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
19:09:56.742 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
19:09:56.743 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:09:56.743 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
19:09:56.743 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
19:09:56.743 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
19:09:56.744 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)
19:09:56.744 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)
19:09:56.744 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
19:09:56.744 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
19:09:56.745 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
19:09:56.745 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
19:09:56.745 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)
19:09:56.745 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)
19:09:56.745 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:09:56.746 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
19:09:56.746 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
19:09:56.746 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
19:09:56.747 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
19:09:56.747 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
19:09:56.747 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
19:09:56.747 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
19:09:56.747 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)
19:09:56.748 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)
19:09:56.748 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:09:56.748 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
19:09:56.748 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
19:09:56.748 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
19:09:56.748 INFO  ProgressMeter -             unmapped              0.0                    10          35294.1
19:09:56.749 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
19:09:56.749 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
19:09:56.754 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:56 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
19:09:56.755 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3320232582740438150.vcf
19:09:56.852 INFO  Funcotator - ------------------------------------------------------------
19:09:56.852 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:56.852 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:56.852 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:56.852 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:56.852 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:56 PM GMT
19:09:56.852 INFO  Funcotator - ------------------------------------------------------------
19:09:56.852 INFO  Funcotator - ------------------------------------------------------------
19:09:56.852 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:56.852 INFO  Funcotator - Picard Version: 3.4.0
19:09:56.852 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:56.852 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:56.852 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:56.852 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:56.852 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:56.852 INFO  Funcotator - Deflater: IntelDeflater
19:09:56.852 INFO  Funcotator - Inflater: IntelInflater
19:09:56.852 INFO  Funcotator - GCS max retries/reopens: 20
19:09:56.852 INFO  Funcotator - Requester pays: disabled
19:09:56.852 INFO  Funcotator - Initializing engine
19:09:56.855 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/non_locatable_proof_input.vcf
19:09:56.856 INFO  Funcotator - Done initializing engine
19:09:56.856 INFO  Funcotator - Validating sequence dictionaries...
19:09:56.856 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:56.856 INFO  Funcotator - Initializing data sources...
19:09:56.856 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:56.856 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:56.856 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
19:09:56.857 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
19:09:56.857 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
19:09:56.857 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
19:09:56.857 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
19:09:56.857 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
19:09:56.858 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
19:09:56.858 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:56.858 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
19:09:56.858 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
19:09:56.858 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
19:09:56.858 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
19:09:56.859 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:56.859 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
19:09:56.859 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
19:09:56.859 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:56.859 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
19:09:56.859 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
19:09:56.878 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
19:09:56.879 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
19:09:56.924 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
19:09:56.925 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
19:09:57.489 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
19:09:57.490 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:57.491 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:57.492 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
19:09:57.495 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:57.497 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:57.497 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:57.498 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:57.526 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:57.527 INFO  DataSourceUtils - 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	2025-05-19 19:09:57	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:57.527 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
19:09:57.565 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
19:09:57.565 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
19:09:57.565 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
19:09:57.573 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:57.573 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
19:09:57.573 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:57.574 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:57.574 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
19:09:57.652 INFO  Funcotator - Initializing Funcotator Engine...
19:09:57.652 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:57.652 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.
19:09:57.652 INFO  Funcotator - Creating a VCF file for output: file:/tmp/non_locatable_proof_input.vcf.funcotator8093793596071395866.vcf
19:09:57.656 INFO  ProgressMeter - Starting traversal
19:09:57.656 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:57.778 INFO  ProgressMeter -             unmapped              0.0                     1            491.8
19:09:57.778 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
19:09:57.778 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:09:57.779 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:57 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3177185280
19:09:57.780 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/non_locatable_proof_input.vcf.funcotator8093793596071395866.vcf
19:09:57.869 INFO  Funcotator - ------------------------------------------------------------
19:09:57.869 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:57.869 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:57.869 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:57.869 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:57.869 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:57 PM GMT
19:09:57.869 INFO  Funcotator - ------------------------------------------------------------
19:09:57.869 INFO  Funcotator - ------------------------------------------------------------
19:09:57.870 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:57.870 INFO  Funcotator - Picard Version: 3.4.0
19:09:57.870 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:57.870 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:57.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:57.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:57.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:57.870 INFO  Funcotator - Deflater: IntelDeflater
19:09:57.870 INFO  Funcotator - Inflater: IntelInflater
19:09:57.870 INFO  Funcotator - GCS max retries/reopens: 20
19:09:57.870 INFO  Funcotator - Requester pays: disabled
19:09:57.870 INFO  Funcotator - Initializing engine
19:09:57.872 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/symbollic_allele_proof_input.vcf
19:09:57.873 INFO  Funcotator - Done initializing engine
19:09:57.873 INFO  Funcotator - Validating sequence dictionaries...
19:09:57.873 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:57.873 INFO  Funcotator - Initializing data sources...
19:09:57.874 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:57.874 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:57.874 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
19:09:57.874 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
19:09:57.874 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
19:09:57.875 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
19:09:57.875 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
19:09:57.875 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
19:09:57.875 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
19:09:57.875 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:57.876 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
19:09:57.876 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
19:09:57.876 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
19:09:57.876 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
19:09:57.876 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:57.877 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
19:09:57.877 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
19:09:57.877 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:57.877 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
19:09:57.877 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
19:09:57.897 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
19:09:57.897 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
19:09:57.943 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
19:09:57.944 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
19:09:58.575 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
19:09:58.575 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:58.576 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:58.578 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
19:09:58.580 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:58.582 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:58.583 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:58.583 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:58.609 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:58.610 INFO  DataSourceUtils - 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	2025-05-19 19:09:58	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:58.610 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
19:09:58.647 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
19:09:58.648 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
19:09:58.648 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
19:09:58.656 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:58.657 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
19:09:58.657 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:58.657 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:58.658 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
19:09:58.733 INFO  Funcotator - Initializing Funcotator Engine...
19:09:58.733 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:09:58.733 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.
19:09:58.733 INFO  Funcotator - Creating a VCF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator8983541258631449509.vcf
19:09:58.737 INFO  ProgressMeter - Starting traversal
19:09:58.737 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:58.744 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1007545-1007545 due to alternate allele: <NON_REF>
19:09:58.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
19:09:58.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
19:09:58.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
19:09:58.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
19:09:58.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
19:09:58.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
19:09:58.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
19:09:58.785 INFO  ProgressMeter -             unmapped              0.0                     2           2500.0
19:09:58.785 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
19:09:58.785 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:09:58.786 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:58 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3177185280
19:09:58.786 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/symbollic_allele_proof_input.vcf.funcotator8983541258631449509.vcf
19:09:58.876 INFO  Funcotator - ------------------------------------------------------------
19:09:58.876 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:09:58.876 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:58.876 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:09:58.876 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:09:58.876 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:09:58 PM GMT
19:09:58.876 INFO  Funcotator - ------------------------------------------------------------
19:09:58.876 INFO  Funcotator - ------------------------------------------------------------
19:09:58.876 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:09:58.876 INFO  Funcotator - Picard Version: 3.4.0
19:09:58.876 INFO  Funcotator - Built for Spark Version: 3.5.0
19:09:58.876 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:58.876 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:58.876 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:58.876 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:58.876 INFO  Funcotator - Deflater: IntelDeflater
19:09:58.876 INFO  Funcotator - Inflater: IntelInflater
19:09:58.876 INFO  Funcotator - GCS max retries/reopens: 20
19:09:58.876 INFO  Funcotator - Requester pays: disabled
19:09:58.876 INFO  Funcotator - Initializing engine
19:09:58.878 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_input_test.vcf
19:09:58.879 INFO  Funcotator - Done initializing engine
19:09:58.880 INFO  Funcotator - Skipping sequence dictionary validation.
19:09:58.880 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:09:58.880 INFO  Funcotator - Initializing data sources...
19:09:58.880 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:09:58.880 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:09:58.880 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
19:09:58.880 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
19:09:58.880 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
19:09:58.881 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
19:09:58.881 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
19:09:58.881 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
19:09:58.881 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
19:09:58.881 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:58.881 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
19:09:58.882 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
19:09:58.882 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
19:09:58.882 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
19:09:58.882 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:58.883 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
19:09:58.883 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
19:09:58.883 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:09:58.883 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
19:09:58.883 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
19:09:58.944 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
19:09:58.945 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
19:09:58.989 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
19:09:58.989 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
19:09:59.615 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
19:09:59.615 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:09:59.616 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:59.618 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
19:09:59.621 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:09:59.623 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:09:59.623 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:59.623 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:09:59.650 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:09:59.650 INFO  DataSourceUtils - 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	2025-05-19 19:09:59	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:09:59.650 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
19:09:59.688 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
19:09:59.689 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
19:09:59.689 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
19:09:59.697 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:09:59.698 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
19:09:59.698 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:09:59.698 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:09:59.699 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
19:09:59.776 INFO  Funcotator - Initializing Funcotator Engine...
19:09:59.776 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:09:59.776 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.
19:09:59.776 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
19:09:59.777 INFO  FuncotatorUtils -     Setting new Variant Classification severity: INTRON = 0
19:09:59.777 INFO  FuncotatorUtils -     Setting new Variant Classification severity: SILENT = 999
19:09:59.777 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9188947431393395827.vcf
19:09:59.780 INFO  ProgressMeter - Starting traversal
19:09:59.781 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:59.814 INFO  ProgressMeter -             unmapped              0.0                     1           1818.2
19:09:59.814 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
19:09:59.814 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:09:59.815 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:09:59 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3229614080
19:09:59.816 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out9188947431393395827.vcf
19:09:59.818 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 19, 2025 at 7:10:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3229614080
[May 19, 2025 at 7:10:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3229614080
19:10:00.216 INFO  Funcotator - ------------------------------------------------------------
19:10:00.216 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:00.216 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:00.216 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:00.216 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:00.216 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:00 PM GMT
19:10:00.216 INFO  Funcotator - ------------------------------------------------------------
19:10:00.216 INFO  Funcotator - ------------------------------------------------------------
19:10:00.216 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:00.216 INFO  Funcotator - Picard Version: 3.4.0
19:10:00.216 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:00.216 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:00.216 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:00.216 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:00.216 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:00.216 INFO  Funcotator - Deflater: IntelDeflater
19:10:00.216 INFO  Funcotator - Inflater: IntelInflater
19:10:00.216 INFO  Funcotator - GCS max retries/reopens: 20
19:10:00.216 INFO  Funcotator - Requester pays: disabled
19:10:00.216 INFO  Funcotator - Initializing engine
19:10:00.217 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
19:10:00.234 INFO  Funcotator - Done initializing engine
19:10:00.234 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:00.234 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:00.234 INFO  Funcotator - Initializing data sources...
19:10:00.234 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:00.234 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:00.234 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
19:10:00.234 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
19:10:00.234 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
19:10:00.234 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:00.234 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
19:10:00.234 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:00.235 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
19:10:00.235 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
19:10:00.236 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
19:10:00.236 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:00.236 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
19:10:00.249 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
19:10:00.263 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
19:10:00.276 INFO  Funcotator - Initializing Funcotator Engine...
19:10:00.281 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:00.281 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7543965613892792275.vcf
19:10:00.296 INFO  ProgressMeter - Starting traversal
19:10:00.296 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:00.322 INFO  ProgressMeter -             unmapped              0.0                   100         230769.2
19:10:00.323 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
19:10:00.323 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
19:10:00.328 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3284140032
19:10:00.329 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7543965613892792275.vcf
19:10:00.429 INFO  Funcotator - ------------------------------------------------------------
19:10:00.429 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:00.429 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:00.429 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:00.429 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:00.429 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:00 PM GMT
19:10:00.429 INFO  Funcotator - ------------------------------------------------------------
19:10:00.429 INFO  Funcotator - ------------------------------------------------------------
19:10:00.429 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:00.429 INFO  Funcotator - Picard Version: 3.4.0
19:10:00.429 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:00.429 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:00.429 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:00.429 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:00.429 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:00.429 INFO  Funcotator - Deflater: IntelDeflater
19:10:00.429 INFO  Funcotator - Inflater: IntelInflater
19:10:00.429 INFO  Funcotator - GCS max retries/reopens: 20
19:10:00.429 INFO  Funcotator - Requester pays: disabled
19:10:00.429 INFO  Funcotator - Initializing engine
19:10:00.432 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/FILTER_test.vcf
19:10:00.432 INFO  Funcotator - Done initializing engine
19:10:00.432 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:00.432 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:00.433 INFO  Funcotator - Initializing data sources...
19:10:00.433 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/
19:10:00.433 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:00.433 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
19:10:00.433 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
19:10:00.433 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
19:10:00.433 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:00.433 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
19:10:00.433 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
19:10:00.434 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
19:10:00.436 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
19:10:00.439 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
19:10:00.441 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
19:10:00.441 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:00.441 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
19:10:00.442 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
19:10:00.442 INFO  Funcotator - Initializing Funcotator Engine...
19:10:00.442 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:00.442 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.
19:10:00.442 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:00.442 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing15894149247429443055.vcf
19:10:00.445 INFO  ProgressMeter - Starting traversal
19:10:00.445 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:00.470 INFO  ProgressMeter -             unmapped              0.0                     1           2400.0
19:10:00.470 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
19:10:00.470 INFO  VcfFuncotationFactory - dbSnp 9606_b150 cache hits/total: 0/1
19:10:00.472 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3284140032
19:10:00.473 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing15894149247429443055.vcf
19:10:00.567 INFO  Funcotator - ------------------------------------------------------------
19:10:00.567 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:00.567 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:00.567 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:00.567 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:00.567 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:00 PM GMT
19:10:00.567 INFO  Funcotator - ------------------------------------------------------------
19:10:00.567 INFO  Funcotator - ------------------------------------------------------------
19:10:00.567 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:00.567 INFO  Funcotator - Picard Version: 3.4.0
19:10:00.568 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:00.568 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:00.568 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:00.568 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:00.568 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:00.568 INFO  Funcotator - Deflater: IntelDeflater
19:10:00.568 INFO  Funcotator - Inflater: IntelInflater
19:10:00.568 INFO  Funcotator - GCS max retries/reopens: 20
19:10:00.568 INFO  Funcotator - Requester pays: disabled
19:10:00.568 INFO  Funcotator - Initializing engine
19:10:00.569 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
19:10:00.570 INFO  Funcotator - Done initializing engine
19:10:00.570 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:00.570 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:00.570 INFO  Funcotator - Initializing data sources...
19:10:00.570 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:00.570 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:00.570 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
19:10:00.570 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
19:10:00.571 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
19:10:00.571 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
19:10:00.571 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
19:10:00.571 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
19:10:00.571 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
19:10:00.572 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:00.572 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
19:10:00.572 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
19:10:00.572 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
19:10:00.572 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
19:10:00.572 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:00.573 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
19:10:00.573 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
19:10:00.573 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:00.573 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
19:10:00.573 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
19:10:00.597 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
19:10:00.597 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
19:10:00.643 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
19:10:00.644 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
19:10:01.233 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
19:10:01.233 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:01.235 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:01.237 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
19:10:01.240 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:01.242 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:01.242 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:01.242 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:01.269 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
19:10:01.269 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
WARNING	2025-05-19 19:10:01	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:01.269 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
19:10:01.307 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
19:10:01.307 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
19:10:01.308 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
19:10:01.344 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:01.344 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
19:10:01.344 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:01.345 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:01.346 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
19:10:01.420 INFO  Funcotator - Initializing Funcotator Engine...
19:10:01.420 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
19:10:01.421 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
19:10:01.421 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
19:10:01.421 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
19:10:01.421 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
19:10:01.422 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
19:10:01.422 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
19:10:01.422 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
19:10:01.422 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
19:10:01.422 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
19:10:01.422 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
19:10:01.422 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
19:10:01.422 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
19:10:01.422 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:01.422 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7717253840529214823.vcf
19:10:01.422 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
19:10:01.423 INFO  ProgressMeter - Starting traversal
19:10:01.423 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:01.457 INFO  ProgressMeter -             unmapped              0.0                     3           5294.1
19:10:01.457 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
19:10:01.457 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:10:01.460 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:01 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3284140032
19:10:01.577 INFO  Funcotator - ------------------------------------------------------------
19:10:01.578 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:01.578 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:01.578 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:01.578 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:01.578 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:01 PM GMT
19:10:01.578 INFO  Funcotator - ------------------------------------------------------------
19:10:01.578 INFO  Funcotator - ------------------------------------------------------------
19:10:01.578 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:01.578 INFO  Funcotator - Picard Version: 3.4.0
19:10:01.578 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:01.578 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:01.578 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:01.578 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:01.578 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:01.578 INFO  Funcotator - Deflater: IntelDeflater
19:10:01.578 INFO  Funcotator - Inflater: IntelInflater
19:10:01.578 INFO  Funcotator - GCS max retries/reopens: 20
19:10:01.578 INFO  Funcotator - Requester pays: disabled
19:10:01.578 INFO  Funcotator - Initializing engine
19:10:01.579 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
19:10:01.579 INFO  Funcotator - Done initializing engine
19:10:01.579 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:01.579 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:01.579 INFO  Funcotator - Initializing data sources...
19:10:01.579 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:01.579 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:01.580 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
19:10:01.580 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
19:10:01.580 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
19:10:01.580 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
19:10:01.580 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
19:10:01.581 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
19:10:01.581 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
19:10:01.581 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:01.581 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
19:10:01.581 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
19:10:01.581 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
19:10:01.582 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
19:10:01.582 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:01.582 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
19:10:01.582 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
19:10:01.582 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:01.582 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
19:10:01.582 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
19:10:01.601 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
19:10:01.602 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
19:10:01.653 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
19:10:01.653 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
19:10:02.303 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
19:10:02.303 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:02.305 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:02.308 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:02.312 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:02.316 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:02.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:02.317 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:02.348 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:02.348 INFO  DataSourceUtils - 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	2025-05-19 19:10:02	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:02.348 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
19:10:02.386 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
19:10:02.387 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
19:10:02.387 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
19:10:02.395 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:02.395 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
19:10:02.395 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:02.396 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:02.396 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
19:10:02.474 INFO  Funcotator - Initializing Funcotator Engine...
19:10:02.474 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:02.474 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:02.474 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9604864321711237448.vcf
19:10:02.475 INFO  ProgressMeter - Starting traversal
19:10:02.475 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:02.580 INFO  ProgressMeter -             unmapped              0.0                     4           2285.7
19:10:02.580 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
19:10:02.580 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:10:02.581 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:02 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2596274176
19:10:02.669 INFO  Funcotator - ------------------------------------------------------------
19:10:02.669 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:02.669 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:02.669 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:02.669 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:02.669 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:02 PM GMT
19:10:02.669 INFO  Funcotator - ------------------------------------------------------------
19:10:02.669 INFO  Funcotator - ------------------------------------------------------------
19:10:02.669 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:02.669 INFO  Funcotator - Picard Version: 3.4.0
19:10:02.669 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:02.669 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:02.669 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:02.669 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:02.669 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:02.669 INFO  Funcotator - Deflater: IntelDeflater
19:10:02.669 INFO  Funcotator - Inflater: IntelInflater
19:10:02.669 INFO  Funcotator - GCS max retries/reopens: 20
19:10:02.669 INFO  Funcotator - Requester pays: disabled
19:10:02.669 INFO  Funcotator - Initializing engine
19:10:02.670 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
19:10:02.671 INFO  Funcotator - Done initializing engine
19:10:02.671 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:02.671 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:02.671 INFO  Funcotator - Initializing data sources...
19:10:02.671 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:02.671 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:02.671 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
19:10:02.672 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
19:10:02.672 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
19:10:02.672 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
19:10:02.672 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
19:10:02.672 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
19:10:02.672 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
19:10:02.673 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
19:10:02.673 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
19:10:02.673 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
19:10:02.673 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
19:10:02.673 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
19:10:02.673 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:02.674 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
19:10:02.674 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
19:10:02.674 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:02.674 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
19:10:02.674 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
19:10:02.693 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
19:10:02.694 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
19:10:02.855 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
19:10:02.855 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
19:10:03.423 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
19:10:03.423 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:03.424 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:03.426 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
19:10:03.429 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:03.431 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:03.431 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:03.431 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:03.458 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:03.458 INFO  DataSourceUtils - 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	2025-05-19 19:10:03	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:03.458 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
19:10:03.495 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
19:10:03.495 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
19:10:03.495 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
19:10:03.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:03.503 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
19:10:03.503 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:03.504 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:03.504 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
19:10:03.580 INFO  Funcotator - Initializing Funcotator Engine...
19:10:03.580 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
19:10:03.580 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
19:10:03.580 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
19:10:03.580 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
19:10:03.580 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
19:10:03.581 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
19:10:03.581 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:03.581 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out825647105510839446.vcf
19:10:03.581 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
19:10:03.582 INFO  ProgressMeter - Starting traversal
19:10:03.582 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:03.608 INFO  ProgressMeter -             unmapped              0.0                     3           6923.1
19:10:03.608 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
19:10:03.608 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:10:03.610 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:03 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2596274176
19:10:03.695 INFO  Funcotator - ------------------------------------------------------------
19:10:03.695 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:03.696 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:03.696 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:03.696 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:03.696 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:03 PM GMT
19:10:03.696 INFO  Funcotator - ------------------------------------------------------------
19:10:03.696 INFO  Funcotator - ------------------------------------------------------------
19:10:03.696 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:03.696 INFO  Funcotator - Picard Version: 3.4.0
19:10:03.696 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:03.696 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:03.696 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:03.696 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:03.696 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:03.696 INFO  Funcotator - Deflater: IntelDeflater
19:10:03.696 INFO  Funcotator - Inflater: IntelInflater
19:10:03.696 INFO  Funcotator - GCS max retries/reopens: 20
19:10:03.696 INFO  Funcotator - Requester pays: disabled
19:10:03.696 INFO  Funcotator - Initializing engine
19:10:03.697 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
19:10:03.698 INFO  Funcotator - Done initializing engine
19:10:03.698 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:03.698 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:03.698 INFO  Funcotator - Initializing data sources...
19:10:03.698 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:03.698 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:03.698 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
19:10:03.698 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
19:10:03.699 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
19:10:03.699 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
19:10:03.699 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
19:10:03.699 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
19:10:03.699 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
19:10:03.699 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:03.700 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
19:10:03.700 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
19:10:03.700 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
19:10:03.700 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
19:10:03.700 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:03.701 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
19:10:03.701 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
19:10:03.701 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:03.701 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
19:10:03.701 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
19:10:03.721 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
19:10:03.721 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
19:10:03.767 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
19:10:03.767 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
19:10:04.372 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
19:10:04.372 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:04.373 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:04.375 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
19:10:04.378 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:04.380 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:04.380 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:04.380 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:04.407 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:04.407 INFO  DataSourceUtils - 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	2025-05-19 19:10:04	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:04.407 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
19:10:04.445 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
19:10:04.445 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
19:10:04.445 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
19:10:04.453 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:04.453 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
19:10:04.453 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:04.454 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:04.454 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
19:10:04.607 INFO  Funcotator - Initializing Funcotator Engine...
19:10:04.607 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:04.607 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:04.607 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12310091168131236124.vcf
19:10:04.608 INFO  ProgressMeter - Starting traversal
19:10:04.608 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:04.711 INFO  ProgressMeter -             unmapped              0.0                     4           2330.1
19:10:04.711 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
19:10:04.711 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:10:04.712 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:04 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2596274176
19:10:04.801 INFO  Funcotator - ------------------------------------------------------------
19:10:04.801 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:04.801 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:04.801 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:04.801 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:04.801 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:04 PM GMT
19:10:04.801 INFO  Funcotator - ------------------------------------------------------------
19:10:04.801 INFO  Funcotator - ------------------------------------------------------------
19:10:04.801 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:04.801 INFO  Funcotator - Picard Version: 3.4.0
19:10:04.801 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:04.801 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:04.801 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:04.801 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:04.801 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:04.801 INFO  Funcotator - Deflater: IntelDeflater
19:10:04.801 INFO  Funcotator - Inflater: IntelInflater
19:10:04.801 INFO  Funcotator - GCS max retries/reopens: 20
19:10:04.801 INFO  Funcotator - Requester pays: disabled
19:10:04.801 INFO  Funcotator - Initializing engine
19:10:04.802 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
19:10:04.803 INFO  Funcotator - Done initializing engine
19:10:04.803 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:04.803 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:04.803 INFO  Funcotator - Initializing data sources...
19:10:04.803 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:04.803 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:04.803 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
19:10:04.803 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
19:10:04.803 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
19:10:04.804 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
19:10:04.804 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
19:10:04.804 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
19:10:04.804 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
19:10:04.804 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:04.804 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
19:10:04.804 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
19:10:04.805 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
19:10:04.805 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
19:10:04.805 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:04.805 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
19:10:04.805 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
19:10:04.805 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:04.805 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
19:10:04.806 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
19:10:04.825 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
19:10:04.825 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
19:10:04.871 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
19:10:04.872 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
19:10:05.620 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
19:10:05.620 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:05.621 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:05.623 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
19:10:05.626 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:05.628 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:05.628 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
19:10:05.629 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:05.655 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:05.655 INFO  DataSourceUtils - 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	2025-05-19 19:10:05	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:05.656 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
19:10:05.746 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
19:10:05.746 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
19:10:05.746 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
19:10:05.754 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:05.755 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
19:10:05.755 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:05.756 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:05.756 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
19:10:05.831 INFO  Funcotator - Initializing Funcotator Engine...
19:10:05.831 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
19:10:05.831 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
19:10:05.832 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
19:10:05.832 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
19:10:05.832 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
19:10:05.832 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:05.832 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out12880473550624303146.maf
19:10:05.833 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
19:10:05.833 INFO  ProgressMeter - Starting traversal
19:10:05.833 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:05.853 INFO  ProgressMeter -             unmapped              0.0                     3           9473.7
19:10:05.853 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
19:10:05.853 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:10:05.853 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2998927360
19:10:05.940 INFO  Funcotator - ------------------------------------------------------------
19:10:05.941 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:05.941 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:05.941 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:05.941 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:05.941 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:05 PM GMT
19:10:05.941 INFO  Funcotator - ------------------------------------------------------------
19:10:05.941 INFO  Funcotator - ------------------------------------------------------------
19:10:05.941 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:05.941 INFO  Funcotator - Picard Version: 3.4.0
19:10:05.941 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:05.941 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:05.941 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:05.941 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:05.941 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:05.941 INFO  Funcotator - Deflater: IntelDeflater
19:10:05.941 INFO  Funcotator - Inflater: IntelInflater
19:10:05.941 INFO  Funcotator - GCS max retries/reopens: 20
19:10:05.941 INFO  Funcotator - Requester pays: disabled
19:10:05.941 INFO  Funcotator - Initializing engine
19:10:05.942 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
19:10:05.942 INFO  Funcotator - Done initializing engine
19:10:05.942 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:05.942 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:05.942 INFO  Funcotator - Initializing data sources...
19:10:05.942 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:05.942 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:05.943 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
19:10:05.943 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
19:10:05.943 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
19:10:05.943 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
19:10:05.943 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
19:10:05.944 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
19:10:05.944 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
19:10:05.944 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
19:10:05.944 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
19:10:05.944 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
19:10:05.944 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
19:10:05.945 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
19:10:05.945 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:05.945 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
19:10:05.945 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
19:10:05.945 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:05.945 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
19:10:05.945 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
19:10:05.965 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
19:10:05.965 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
19:10:06.012 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
19:10:06.013 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
19:10:06.612 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
19:10:06.612 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:06.613 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:06.615 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
19:10:06.618 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:06.620 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:06.620 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:06.621 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:06.647 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
19:10:06.647 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
WARNING	2025-05-19 19:10:06	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:06.648 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
19:10:06.685 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
19:10:06.686 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
19:10:06.686 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
19:10:06.694 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:06.694 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
19:10:06.694 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:06.695 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:06.695 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
19:10:06.836 INFO  Funcotator - Initializing Funcotator Engine...
19:10:06.836 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:06.836 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:06.836 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out17239396957589360237.maf
19:10:06.836 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
19:10:06.836 INFO  ProgressMeter - Starting traversal
19:10:06.836 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:06.939 INFO  ProgressMeter -             unmapped              0.0                     4           2330.1
19:10:06.939 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
19:10:06.939 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:10:06.939 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:06 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2998927360
19:10:07.028 INFO  Funcotator - ------------------------------------------------------------
19:10:07.028 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:07.028 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:07.029 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:07.029 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:07.029 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:07 PM GMT
19:10:07.029 INFO  Funcotator - ------------------------------------------------------------
19:10:07.029 INFO  Funcotator - ------------------------------------------------------------
19:10:07.029 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:07.029 INFO  Funcotator - Picard Version: 3.4.0
19:10:07.029 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:07.029 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:07.029 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:07.029 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:07.029 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:07.029 INFO  Funcotator - Deflater: IntelDeflater
19:10:07.029 INFO  Funcotator - Inflater: IntelInflater
19:10:07.029 INFO  Funcotator - GCS max retries/reopens: 20
19:10:07.029 INFO  Funcotator - Requester pays: disabled
19:10:07.029 INFO  Funcotator - Initializing engine
19:10:07.030 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
19:10:07.030 INFO  Funcotator - Done initializing engine
19:10:07.030 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:07.030 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:07.030 INFO  Funcotator - Initializing data sources...
19:10:07.030 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:07.030 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:07.031 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
19:10:07.031 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
19:10:07.031 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
19:10:07.031 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
19:10:07.031 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
19:10:07.031 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
19:10:07.031 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
19:10:07.032 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:07.032 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
19:10:07.032 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
19:10:07.032 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
19:10:07.032 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
19:10:07.032 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:07.033 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
19:10:07.033 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
19:10:07.033 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:07.033 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
19:10:07.033 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
19:10:07.052 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
19:10:07.053 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
19:10:07.098 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
19:10:07.099 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
19:10:07.784 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
19:10:07.784 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:07.785 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:07.787 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
19:10:07.790 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:07.792 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:07.792 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:07.792 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:07.819 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:07.819 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-19 19:10:07	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:07.819 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
19:10:07.857 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
19:10:07.857 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
19:10:07.858 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
19:10:07.866 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:07.866 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
19:10:07.866 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:07.867 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:07.867 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
19:10:07.944 INFO  Funcotator - Initializing Funcotator Engine...
19:10:07.944 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
19:10:07.945 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
19:10:07.945 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
19:10:07.945 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
19:10:07.945 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
19:10:07.945 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:07.945 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6347546439160922497.maf
19:10:07.946 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
19:10:07.946 INFO  ProgressMeter - Starting traversal
19:10:07.946 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:07.964 INFO  ProgressMeter -             unmapped              0.0                     3          10000.0
19:10:07.964 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
19:10:07.964 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:10:07.965 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:07 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3114270720
19:10:08.086 INFO  Funcotator - ------------------------------------------------------------
19:10:08.086 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:08.086 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:08.086 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:08.086 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:08.086 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:08 PM GMT
19:10:08.086 INFO  Funcotator - ------------------------------------------------------------
19:10:08.086 INFO  Funcotator - ------------------------------------------------------------
19:10:08.086 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:08.086 INFO  Funcotator - Picard Version: 3.4.0
19:10:08.086 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:08.086 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:08.086 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:08.086 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:08.086 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:08.086 INFO  Funcotator - Deflater: IntelDeflater
19:10:08.086 INFO  Funcotator - Inflater: IntelInflater
19:10:08.086 INFO  Funcotator - GCS max retries/reopens: 20
19:10:08.086 INFO  Funcotator - Requester pays: disabled
19:10:08.086 INFO  Funcotator - Initializing engine
19:10:08.087 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
19:10:08.088 INFO  Funcotator - Done initializing engine
19:10:08.088 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:08.088 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:08.088 INFO  Funcotator - Initializing data sources...
19:10:08.088 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:08.088 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:08.088 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
19:10:08.088 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
19:10:08.088 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
19:10:08.089 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
19:10:08.089 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
19:10:08.089 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
19:10:08.089 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
19:10:08.089 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:08.089 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
19:10:08.089 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
19:10:08.090 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
19:10:08.090 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
19:10:08.090 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:08.090 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
19:10:08.090 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
19:10:08.090 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:08.090 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
19:10:08.090 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
19:10:08.110 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
19:10:08.110 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
19:10:08.156 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
19:10:08.157 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
19:10:08.774 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
19:10:08.774 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:08.775 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:08.777 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
19:10:08.779 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:08.781 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:08.782 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:08.782 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:08.809 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:08.809 INFO  DataSourceUtils - 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	2025-05-19 19:10:08	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:08.809 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
19:10:08.847 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
19:10:08.847 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
19:10:08.847 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
19:10:08.855 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:08.856 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
19:10:08.856 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:08.857 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:08.857 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
19:10:08.932 INFO  Funcotator - Initializing Funcotator Engine...
19:10:08.932 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:08.932 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:08.932 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6976274627238507130.maf
19:10:08.932 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
19:10:08.933 INFO  ProgressMeter - Starting traversal
19:10:08.933 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:09.035 INFO  ProgressMeter -             unmapped              0.0                     4           2352.9
19:10:09.035 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
19:10:09.035 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
19:10:09.035 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:09 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3114270720
19:10:09.164 INFO  Funcotator - ------------------------------------------------------------
19:10:09.164 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:09.164 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:09.164 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:09.164 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:09.164 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:09 PM GMT
19:10:09.164 INFO  Funcotator - ------------------------------------------------------------
19:10:09.164 INFO  Funcotator - ------------------------------------------------------------
19:10:09.164 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:09.164 INFO  Funcotator - Picard Version: 3.4.0
19:10:09.164 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:09.164 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:09.164 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:09.164 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:09.164 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:09.164 INFO  Funcotator - Deflater: IntelDeflater
19:10:09.164 INFO  Funcotator - Inflater: IntelInflater
19:10:09.164 INFO  Funcotator - GCS max retries/reopens: 20
19:10:09.164 INFO  Funcotator - Requester pays: disabled
19:10:09.164 INFO  Funcotator - Initializing engine
19:10:09.165 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
19:10:09.193 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
19:10:09.193 INFO  Funcotator - Done initializing engine
19:10:09.193 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:09.193 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:09.193 INFO  Funcotator - Initializing data sources...
19:10:09.193 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
19:10:09.193 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:09.193 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
19:10:09.193 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
19:10:09.193 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
19:10:09.194 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:09.194 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
19:10:09.194 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:09.194 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
19:10:09.202 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
19:10:09.210 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
19:10:09.218 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
19:10:09.218 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:09.219 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
19:10:09.220 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
19:10:09.220 INFO  Funcotator - Initializing Funcotator Engine...
19:10:09.224 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:09.224 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out1871659471342290391.vcf
19:10:09.236 INFO  ProgressMeter - Starting traversal
19:10:09.236 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:09.248 INFO  ProgressMeter -             unmapped              0.0                    32         160000.0
19:10:09.248 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
19:10:09.248 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
19:10:09.253 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:09 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3114270720
19:10:09.338 INFO  Funcotator - ------------------------------------------------------------
19:10:09.338 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:09.338 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:09.338 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:09.338 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:09.338 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:09 PM GMT
19:10:09.338 INFO  Funcotator - ------------------------------------------------------------
19:10:09.338 INFO  Funcotator - ------------------------------------------------------------
19:10:09.339 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:09.339 INFO  Funcotator - Picard Version: 3.4.0
19:10:09.339 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:09.339 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:09.339 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:09.339 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:09.339 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:09.339 INFO  Funcotator - Deflater: IntelDeflater
19:10:09.339 INFO  Funcotator - Inflater: IntelInflater
19:10:09.339 INFO  Funcotator - GCS max retries/reopens: 20
19:10:09.339 INFO  Funcotator - Requester pays: disabled
19:10:09.339 INFO  Funcotator - Initializing engine
19:10:09.340 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
19:10:09.361 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
19:10:09.361 INFO  Funcotator - Done initializing engine
19:10:09.361 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:09.361 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:09.361 INFO  Funcotator - Initializing data sources...
19:10:09.361 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
19:10:09.361 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:09.361 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
19:10:09.362 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
19:10:09.362 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
19:10:09.362 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:09.362 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
19:10:09.362 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:09.362 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
19:10:09.370 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
19:10:09.378 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
19:10:09.386 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
19:10:09.386 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:09.387 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
19:10:09.387 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
19:10:09.387 INFO  Funcotator - Initializing Funcotator Engine...
19:10:09.392 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:09.392 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out14119833147263415276.vcf
19:10:09.403 INFO  ProgressMeter - Starting traversal
19:10:09.403 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:09.414 INFO  ProgressMeter -             unmapped              0.0                    32         174545.5
19:10:09.414 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
19:10:09.414 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
19:10:09.419 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:09 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3114270720
19:10:09.420 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out1871659471342290391.vcf
19:10:09.429 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out14119833147263415276.vcf
19:10:09.585 INFO  Funcotator - ------------------------------------------------------------
19:10:09.585 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:09.585 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:09.585 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:09.585 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:09.585 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:09 PM GMT
19:10:09.585 INFO  Funcotator - ------------------------------------------------------------
19:10:09.585 INFO  Funcotator - ------------------------------------------------------------
19:10:09.586 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:09.586 INFO  Funcotator - Picard Version: 3.4.0
19:10:09.586 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:09.586 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:09.586 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:09.586 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:09.586 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:09.586 INFO  Funcotator - Deflater: IntelDeflater
19:10:09.586 INFO  Funcotator - Inflater: IntelInflater
19:10:09.586 INFO  Funcotator - GCS max retries/reopens: 20
19:10:09.586 INFO  Funcotator - Requester pays: disabled
19:10:09.586 INFO  Funcotator - Initializing engine
19:10:09.587 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf
19:10:09.589 INFO  Funcotator - Done initializing engine
19:10:09.589 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:09.589 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:09.589 INFO  Funcotator - Initializing data sources...
19:10:09.589 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:09.589 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:09.590 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
19:10:09.590 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
19:10:09.590 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
19:10:09.590 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:09.590 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
19:10:09.590 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:09.591 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
19:10:09.591 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
19:10:09.591 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
19:10:09.591 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:09.592 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
19:10:09.592 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
19:10:09.594 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
19:10:09.594 INFO  Funcotator - Initializing Funcotator Engine...
19:10:09.594 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:09.594 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.
19:10:09.595 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out11303919251444431966.maf
19:10:09.595 INFO  ProgressMeter - Starting traversal
19:10:09.595 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:09.597 WARN  MafOutputRenderer - 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
19:10:09.597 WARN  MafOutputRenderer - 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
19:10:09.597 WARN  MafOutputRenderer - 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
19:10:09.599 WARN  MafOutputRenderer - 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=
19:10:09.599 WARN  MafOutputRenderer - 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=
19:10:09.600 WARN  MafOutputRenderer - 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=
19:10:09.600 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
19:10:09.600 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
19:10:09.600 WARN  Funcotator - ================================================================================
19:10:09.600 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
19:10:09.600 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
19:10:09.600 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
19:10:09.600 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
19:10:09.600 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
19:10:09.600 WARN  Funcotator -                                                   |___/                         ?[0;0m
19:10:09.600 WARN  Funcotator - --------------------------------------------------------------------------------
19:10:09.600 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
19:10:09.600 WARN  Funcotator -  run was misconfigured.     
19:10:09.600 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
19:10:09.600 WARN  Funcotator - ================================================================================
19:10:09.600 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
19:10:09.600 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:09 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3166699520
19:10:09.690 INFO  Funcotator - ------------------------------------------------------------
19:10:09.691 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:09.691 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:09.691 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:09.691 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:09.691 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:09 PM GMT
19:10:09.691 INFO  Funcotator - ------------------------------------------------------------
19:10:09.691 INFO  Funcotator - ------------------------------------------------------------
19:10:09.691 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:09.691 INFO  Funcotator - Picard Version: 3.4.0
19:10:09.691 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:09.691 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:09.691 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:09.691 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:09.691 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:09.691 INFO  Funcotator - Deflater: IntelDeflater
19:10:09.691 INFO  Funcotator - Inflater: IntelInflater
19:10:09.691 INFO  Funcotator - GCS max retries/reopens: 20
19:10:09.691 INFO  Funcotator - Requester pays: disabled
19:10:09.691 INFO  Funcotator - Initializing engine
19:10:09.692 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf
19:10:09.693 INFO  Funcotator - Done initializing engine
19:10:09.693 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:09.693 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:09.693 INFO  Funcotator - Initializing data sources...
19:10:09.693 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:09.693 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:09.693 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
19:10:09.693 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
19:10:09.694 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
19:10:09.694 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:09.694 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
19:10:09.694 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:09.694 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
19:10:09.695 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
19:10:09.695 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
19:10:09.695 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:09.695 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
19:10:09.696 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
19:10:09.697 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
19:10:09.698 INFO  Funcotator - Initializing Funcotator Engine...
19:10:09.698 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:09.698 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.
19:10:09.698 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5269868692229640720.maf
19:10:09.699 INFO  ProgressMeter - Starting traversal
19:10:09.699 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:09.700 WARN  MafOutputRenderer - 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
19:10:09.701 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
19:10:09.701 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
19:10:09.703 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:09.703 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:09.705 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:09.705 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
19:10:09.705 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
19:10:09.705 WARN  Funcotator - ================================================================================
19:10:09.705 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
19:10:09.705 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
19:10:09.705 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
19:10:09.705 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
19:10:09.705 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
19:10:09.705 WARN  Funcotator -                                                   |___/                         ?[0;0m
19:10:09.705 WARN  Funcotator - --------------------------------------------------------------------------------
19:10:09.705 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
19:10:09.705 WARN  Funcotator -  run was misconfigured.     
19:10:09.705 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
19:10:09.705 WARN  Funcotator - ================================================================================
19:10:09.705 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
19:10:09.705 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:09 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3166699520
19:10:09.795 INFO  Funcotator - ------------------------------------------------------------
19:10:09.795 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:09.795 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:09.795 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:09.795 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:09.795 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:09 PM GMT
19:10:09.795 INFO  Funcotator - ------------------------------------------------------------
19:10:09.795 INFO  Funcotator - ------------------------------------------------------------
19:10:09.795 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:09.795 INFO  Funcotator - Picard Version: 3.4.0
19:10:09.795 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:09.795 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:09.795 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:09.795 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:09.795 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:09.795 INFO  Funcotator - Deflater: IntelDeflater
19:10:09.795 INFO  Funcotator - Inflater: IntelInflater
19:10:09.795 INFO  Funcotator - GCS max retries/reopens: 20
19:10:09.795 INFO  Funcotator - Requester pays: disabled
19:10:09.795 INFO  Funcotator - Initializing engine
19:10:09.796 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
19:10:09.797 INFO  Funcotator - Done initializing engine
19:10:09.797 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:09.797 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:09.797 INFO  Funcotator - Initializing data sources...
19:10:09.797 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:09.797 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:09.797 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
19:10:09.797 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
19:10:09.798 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
19:10:09.798 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:09.798 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
19:10:09.798 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:09.798 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
19:10:09.799 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
19:10:09.799 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
19:10:09.799 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:09.799 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
19:10:09.800 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
19:10:09.801 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
19:10:09.802 INFO  Funcotator - Initializing Funcotator Engine...
19:10:09.802 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:09.802 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
19:10:09.802 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out18153826080053588295.maf
19:10:09.803 INFO  ProgressMeter - Starting traversal
19:10:09.803 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:09.804 WARN  MafOutputRenderer - 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
19:10:09.805 WARN  MafOutputRenderer - 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
19:10:09.805 WARN  MafOutputRenderer - 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
19:10:09.806 WARN  MafOutputRenderer - 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=
19:10:09.806 WARN  MafOutputRenderer - 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=
19:10:09.808 WARN  MafOutputRenderer - 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=
19:10:09.808 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
19:10:09.808 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
19:10:09.808 WARN  Funcotator - ================================================================================
19:10:09.808 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
19:10:09.808 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
19:10:09.808 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
19:10:09.808 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
19:10:09.808 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
19:10:09.808 WARN  Funcotator -                                                   |___/                         ?[0;0m
19:10:09.808 WARN  Funcotator - --------------------------------------------------------------------------------
19:10:09.808 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
19:10:09.808 WARN  Funcotator -  run was misconfigured.     
19:10:09.808 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
19:10:09.808 WARN  Funcotator - ================================================================================
19:10:09.808 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
19:10:09.808 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:09 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3166699520
19:10:09.896 INFO  Funcotator - ------------------------------------------------------------
19:10:09.896 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:09.896 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:09.896 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:09.896 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:09.896 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:09 PM GMT
19:10:09.896 INFO  Funcotator - ------------------------------------------------------------
19:10:09.896 INFO  Funcotator - ------------------------------------------------------------
19:10:09.896 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:09.896 INFO  Funcotator - Picard Version: 3.4.0
19:10:09.896 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:09.896 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:09.896 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:09.896 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:09.896 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:09.896 INFO  Funcotator - Deflater: IntelDeflater
19:10:09.896 INFO  Funcotator - Inflater: IntelInflater
19:10:09.896 INFO  Funcotator - GCS max retries/reopens: 20
19:10:09.896 INFO  Funcotator - Requester pays: disabled
19:10:09.896 INFO  Funcotator - Initializing engine
19:10:09.898 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
19:10:09.899 INFO  Funcotator - Done initializing engine
19:10:09.899 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:09.899 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:09.899 INFO  Funcotator - Initializing data sources...
19:10:09.899 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:09.899 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:09.900 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
19:10:09.900 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
19:10:09.900 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
19:10:09.900 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:09.900 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
19:10:09.900 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:09.901 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
19:10:09.901 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
19:10:09.902 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
19:10:09.902 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:09.902 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
19:10:09.903 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
19:10:09.905 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
19:10:09.905 INFO  Funcotator - Initializing Funcotator Engine...
19:10:09.906 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:09.906 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.
19:10:09.906 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out16536621229739417280.maf
19:10:09.906 INFO  ProgressMeter - Starting traversal
19:10:09.906 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:09.907 WARN  MafOutputRenderer - 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
19:10:09.908 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
19:10:09.908 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
19:10:09.909 WARN  MafOutputRenderer - 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=
19:10:09.909 WARN  MafOutputRenderer - 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=
19:10:09.911 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:09.911 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
19:10:09.911 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
19:10:09.911 WARN  Funcotator - ================================================================================
19:10:09.911 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
19:10:09.911 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
19:10:09.911 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
19:10:09.911 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
19:10:09.911 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
19:10:09.911 WARN  Funcotator -                                                   |___/                         ?[0;0m
19:10:09.911 WARN  Funcotator - --------------------------------------------------------------------------------
19:10:09.911 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
19:10:09.911 WARN  Funcotator -  run was misconfigured.     
19:10:09.911 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
19:10:09.911 WARN  Funcotator - ================================================================================
19:10:09.911 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
19:10:09.911 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:09 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3166699520
19:10:09.998 INFO  Funcotator - ------------------------------------------------------------
19:10:09.998 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:09.998 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:09.998 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:09.998 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:09.998 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:09 PM GMT
19:10:09.998 INFO  Funcotator - ------------------------------------------------------------
19:10:09.998 INFO  Funcotator - ------------------------------------------------------------
19:10:09.998 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:09.998 INFO  Funcotator - Picard Version: 3.4.0
19:10:09.998 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:09.998 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:09.998 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:09.998 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:09.998 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:09.998 INFO  Funcotator - Deflater: IntelDeflater
19:10:09.998 INFO  Funcotator - Inflater: IntelInflater
19:10:09.998 INFO  Funcotator - GCS max retries/reopens: 20
19:10:09.998 INFO  Funcotator - Requester pays: disabled
19:10:09.998 INFO  Funcotator - Initializing engine
19:10:09.999 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
19:10:10.002 INFO  Funcotator - Done initializing engine
19:10:10.002 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:10.002 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:10.002 INFO  Funcotator - Initializing data sources...
19:10:10.002 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:10.002 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:10.002 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
19:10:10.002 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
19:10:10.002 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
19:10:10.002 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:10.002 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
19:10:10.002 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:10.003 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
19:10:10.003 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
19:10:10.004 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
19:10:10.004 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:10.004 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
19:10:10.005 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
19:10:10.007 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
19:10:10.007 INFO  Funcotator - Initializing Funcotator Engine...
19:10:10.008 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:10.008 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.
19:10:10.008 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3079782082739161957.vcf
19:10:10.011 INFO  ProgressMeter - Starting traversal
19:10:10.011 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:10.020 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
19:10:10.020 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
19:10:10.020 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
19:10:10.023 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:10 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3166699520
19:10:10.023 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3079782082739161957.vcf
19:10:10.113 INFO  Funcotator - ------------------------------------------------------------
19:10:10.113 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:10.113 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:10.113 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:10.113 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:10.113 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:10 PM GMT
19:10:10.113 INFO  Funcotator - ------------------------------------------------------------
19:10:10.113 INFO  Funcotator - ------------------------------------------------------------
19:10:10.113 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:10.113 INFO  Funcotator - Picard Version: 3.4.0
19:10:10.113 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:10.113 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:10.113 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:10.113 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:10.113 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:10.113 INFO  Funcotator - Deflater: IntelDeflater
19:10:10.113 INFO  Funcotator - Inflater: IntelInflater
19:10:10.113 INFO  Funcotator - GCS max retries/reopens: 20
19:10:10.113 INFO  Funcotator - Requester pays: disabled
19:10:10.113 INFO  Funcotator - Initializing engine
19:10:10.115 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/Three_sample_somatic.vcf
19:10:10.116 INFO  Funcotator - Done initializing engine
19:10:10.116 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:10.116 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:10.116 INFO  Funcotator - Initializing data sources...
19:10:10.116 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:10.116 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:10.116 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
19:10:10.116 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
19:10:10.116 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
19:10:10.116 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:10.116 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
19:10:10.116 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:10.117 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
19:10:10.117 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
19:10:10.117 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
19:10:10.117 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:10.118 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
19:10:10.118 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
19:10:10.120 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
19:10:10.121 INFO  Funcotator - Initializing Funcotator Engine...
19:10:10.121 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:10.121 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.
19:10:10.121 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6438328314001456247.maf
19:10:10.121 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
19:10:10.121 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:10 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3166699520
19:10:10.203 INFO  Funcotator - ------------------------------------------------------------
19:10:10.203 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:10.203 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:10.203 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:10.203 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:10.203 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:10 PM GMT
19:10:10.203 INFO  Funcotator - ------------------------------------------------------------
19:10:10.203 INFO  Funcotator - ------------------------------------------------------------
19:10:10.203 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:10.203 INFO  Funcotator - Picard Version: 3.4.0
19:10:10.203 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:10.203 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:10.203 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:10.203 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:10.203 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:10.203 INFO  Funcotator - Deflater: IntelDeflater
19:10:10.203 INFO  Funcotator - Inflater: IntelInflater
19:10:10.203 INFO  Funcotator - GCS max retries/reopens: 20
19:10:10.203 INFO  Funcotator - Requester pays: disabled
19:10:10.203 INFO  Funcotator - Initializing engine
19:10:10.204 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
19:10:10.216 INFO  Funcotator - Done initializing engine
19:10:10.216 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:10.216 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:10.216 INFO  Funcotator - Initializing data sources...
19:10:10.216 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:10.216 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:10.217 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
19:10:10.217 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
19:10:10.217 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
19:10:10.217 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:10.217 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
19:10:10.217 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:10.218 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
19:10:10.218 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
19:10:10.219 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
19:10:10.219 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:10.220 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
19:10:10.233 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
19:10:10.244 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
19:10:10.252 INFO  Funcotator - Initializing Funcotator Engine...
19:10:10.258 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:10.258 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8321190085093640697.maf
19:10:10.258 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
19:10:10.259 INFO  ProgressMeter - Starting traversal
19:10:10.259 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:10.261 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)
19:10:10.261 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)
19:10:10.261 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:10:10.261 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
19:10:10.262 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
19:10:10.262 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
19:10:10.263 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199000 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+
19:10:10.266 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:10:10.266 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
19:10:10.266 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
19:10:10.266 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
19:10:10.267 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199001 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+
19:10:10.267 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)
19:10:10.267 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)
19:10:10.267 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:10:10.267 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
19:10:10.268 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
19:10:10.268 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
19:10:10.268 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199002 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+
19:10:10.268 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)
19:10:10.268 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)
19:10:10.268 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
19:10:10.269 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
19:10:10.269 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
19:10:10.269 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
19:10:10.269 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199003 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+
19:10:10.270 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:10:10.270 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
19:10:10.270 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
19:10:10.270 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
19:10:10.270 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199004 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+
19:10:10.271 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:10:10.271 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
19:10:10.271 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
19:10:10.271 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
19:10:10.271 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199005 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=
19:10:10.271 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)
19:10:10.272 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)
19:10:10.272 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
19:10:10.272 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
19:10:10.272 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
19:10:10.272 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
19:10:10.272 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199006 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=
19:10:10.272 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)
19:10:10.273 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)
19:10:10.273 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:10:10.273 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
19:10:10.273 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
19:10:10.273 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
19:10:10.273 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199007 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+
19:10:10.274 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
19:10:10.274 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
19:10:10.274 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
19:10:10.274 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
19:10:10.274 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199008 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+
19:10:10.275 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)
19:10:10.275 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)
19:10:10.275 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
19:10:10.275 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
19:10:10.275 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
19:10:10.275 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
19:10:10.275 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199009 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=
19:10:10.276 INFO  ProgressMeter -             unmapped              0.0                    10          35294.1
19:10:10.276 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
19:10:10.276 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
19:10:10.276 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:10 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3166699520
[May 19, 2025 at 7:10:10 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3166699520
19:10:10.461 INFO  Funcotator - ------------------------------------------------------------
19:10:10.461 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:10.461 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:10.461 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:10.461 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:10.461 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:10 PM GMT
19:10:10.461 INFO  Funcotator - ------------------------------------------------------------
19:10:10.461 INFO  Funcotator - ------------------------------------------------------------
19:10:10.462 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:10.462 INFO  Funcotator - Picard Version: 3.4.0
19:10:10.462 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:10.462 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:10.462 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:10.462 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:10.462 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:10.462 INFO  Funcotator - Deflater: IntelDeflater
19:10:10.462 INFO  Funcotator - Inflater: IntelInflater
19:10:10.462 INFO  Funcotator - GCS max retries/reopens: 20
19:10:10.462 INFO  Funcotator - Requester pays: disabled
19:10:10.462 INFO  Funcotator - Initializing engine
19:10:10.463 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
19:10:10.464 INFO  Funcotator - Done initializing engine
19:10:10.464 INFO  Funcotator - Validating sequence dictionaries...
19:10:10.465 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:10 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3166699520
19:10:10.548 INFO  Funcotator - ------------------------------------------------------------
19:10:10.548 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:10.548 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:10.548 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:10.548 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:10.548 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:10 PM GMT
19:10:10.548 INFO  Funcotator - ------------------------------------------------------------
19:10:10.548 INFO  Funcotator - ------------------------------------------------------------
19:10:10.548 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:10.548 INFO  Funcotator - Picard Version: 3.4.0
19:10:10.548 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:10.548 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:10.548 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:10.548 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:10.548 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:10.548 INFO  Funcotator - Deflater: IntelDeflater
19:10:10.548 INFO  Funcotator - Inflater: IntelInflater
19:10:10.548 INFO  Funcotator - GCS max retries/reopens: 20
19:10:10.548 INFO  Funcotator - Requester pays: disabled
19:10:10.548 INFO  Funcotator - Initializing engine
19:10:10.550 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
19:10:10.551 INFO  Funcotator - Done initializing engine
19:10:10.551 INFO  Funcotator - Validating sequence dictionaries...
19:10:10.551 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:10.551 INFO  Funcotator - Initializing data sources...
19:10:10.551 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:10.551 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:10.552 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
19:10:10.552 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
19:10:10.552 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
19:10:10.552 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
19:10:10.552 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
19:10:10.552 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
19:10:10.552 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
19:10:10.553 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:10.553 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
19:10:10.553 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
19:10:10.553 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
19:10:10.553 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
19:10:10.553 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:10.554 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
19:10:10.554 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
19:10:10.554 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:10.554 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
19:10:10.554 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
19:10:10.573 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
19:10:10.573 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
19:10:10.619 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
19:10:10.619 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
19:10:11.235 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
19:10:11.235 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:11.236 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:11.238 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
19:10:11.241 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:11.243 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:11.243 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:11.243 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:11.270 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:11.271 INFO  DataSourceUtils - 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	2025-05-19 19:10:11	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:11.271 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
19:10:11.309 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
19:10:11.309 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
19:10:11.310 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
19:10:11.318 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:11.318 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:11.318 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:11.319 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:11.319 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
19:10:11.432 INFO  Funcotator - Initializing Funcotator Engine...
19:10:11.432 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:10:11.432 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.
19:10:11.432 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator8678398356790904777.vcf
19:10:11.433 INFO  ProgressMeter - Starting traversal
19:10:11.433 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:13.424 INFO  ProgressMeter -             unmapped              0.0                   198           5969.8
19:10:13.424 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
19:10:13.424 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
19:10:13.433 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:13 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2887778304
19:10:13.527 INFO  Funcotator - ------------------------------------------------------------
19:10:13.527 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:13.527 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:13.527 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:13.527 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:13.527 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:13 PM GMT
19:10:13.527 INFO  Funcotator - ------------------------------------------------------------
19:10:13.527 INFO  Funcotator - ------------------------------------------------------------
19:10:13.527 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:13.527 INFO  Funcotator - Picard Version: 3.4.0
19:10:13.527 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:13.527 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:13.527 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:13.528 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:13.528 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:13.528 INFO  Funcotator - Deflater: IntelDeflater
19:10:13.528 INFO  Funcotator - Inflater: IntelInflater
19:10:13.528 INFO  Funcotator - GCS max retries/reopens: 20
19:10:13.528 INFO  Funcotator - Requester pays: disabled
19:10:13.528 INFO  Funcotator - Initializing engine
19:10:13.530 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
19:10:13.531 INFO  Funcotator - Done initializing engine
19:10:13.531 INFO  Funcotator - Validating sequence dictionaries...
19:10:13.531 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:13.531 INFO  Funcotator - Initializing data sources...
19:10:13.531 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:13.531 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:13.531 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
19:10:13.532 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
19:10:13.532 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
19:10:13.532 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
19:10:13.532 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
19:10:13.532 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
19:10:13.532 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
19:10:13.533 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:13.533 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
19:10:13.533 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
19:10:13.533 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
19:10:13.533 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
19:10:13.533 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:13.534 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
19:10:13.534 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
19:10:13.534 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:13.534 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
19:10:13.534 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
19:10:13.554 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
19:10:13.554 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
19:10:13.599 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
19:10:13.599 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
19:10:14.182 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
19:10:14.182 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:14.182 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:14.184 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
19:10:14.187 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:14.189 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:14.189 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:14.190 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:14.216 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:14.216 INFO  DataSourceUtils - 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	2025-05-19 19:10:14	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:14.216 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
19:10:14.255 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
19:10:14.255 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
19:10:14.255 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
19:10:14.263 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:14.264 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
19:10:14.264 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:14.264 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:14.265 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
19:10:14.342 INFO  Funcotator - Initializing Funcotator Engine...
19:10:14.342 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
19:10:14.342 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.
19:10:14.342 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator11879074783486041510.maf
19:10:14.342 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
19:10:14.343 INFO  ProgressMeter - Starting traversal
19:10:14.343 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:16.341 INFO  ProgressMeter -             unmapped              0.0                   198           5945.9
19:10:16.341 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
19:10:16.341 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
19:10:16.341 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:16 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2887778304
19:10:16.427 INFO  Funcotator - ------------------------------------------------------------
19:10:16.427 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:16.427 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:16.427 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:16.427 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:16.427 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:16 PM GMT
19:10:16.427 INFO  Funcotator - ------------------------------------------------------------
19:10:16.427 INFO  Funcotator - ------------------------------------------------------------
19:10:16.427 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:16.427 INFO  Funcotator - Picard Version: 3.4.0
19:10:16.427 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:16.427 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:16.427 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:16.427 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:16.427 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:16.427 INFO  Funcotator - Deflater: IntelDeflater
19:10:16.427 INFO  Funcotator - Inflater: IntelInflater
19:10:16.427 INFO  Funcotator - GCS max retries/reopens: 20
19:10:16.427 INFO  Funcotator - Requester pays: disabled
19:10:16.427 INFO  Funcotator - Initializing engine
19:10:16.453 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/badDataOneAlleleDepthValue_hg38.vcf
19:10:16.473 INFO  Funcotator - Done initializing engine
19:10:16.473 INFO  Funcotator - Validating sequence dictionaries...
19:10:16.479 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:16.479 INFO  Funcotator - Initializing data sources...
19:10:16.479 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:16.479 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:16.480 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
19:10:16.480 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
19:10:16.480 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
19:10:16.480 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
19:10:16.480 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
19:10:16.480 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
19:10:16.480 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
19:10:16.481 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
19:10:16.481 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
19:10:16.481 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
19:10:16.481 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
19:10:16.481 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
19:10:16.481 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
19:10:16.481 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:16.481 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
19:10:16.482 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
19:10:16.500 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
19:10:16.500 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
19:10:16.545 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
19:10:16.546 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
19:10:17.120 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
19:10:17.120 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:17.121 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
19:10:17.122 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
19:10:17.124 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
19:10:17.125 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
19:10:17.188 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
19:10:17.189 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
19:10:17.189 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
19:10:17.197 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
19:10:17.197 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:17.198 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
19:10:17.198 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
19:10:17.199 INFO  Funcotator - Initializing Funcotator Engine...
19:10:17.202 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:17.202 INFO  Funcotator - Creating a MAF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator5188514839731129908.vcf
19:10:17.203 INFO  ProgressMeter - Starting traversal
19:10:17.203 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:17.208 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
19:10:17.211 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2887778304
19:10:17.294 INFO  Funcotator - ------------------------------------------------------------
19:10:17.294 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:17.294 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:17.294 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:17.294 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:17.294 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:17 PM GMT
19:10:17.294 INFO  Funcotator - ------------------------------------------------------------
19:10:17.294 INFO  Funcotator - ------------------------------------------------------------
19:10:17.294 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:17.294 INFO  Funcotator - Picard Version: 3.4.0
19:10:17.294 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:17.294 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:17.294 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:17.294 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:17.294 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:17.294 INFO  Funcotator - Deflater: IntelDeflater
19:10:17.295 INFO  Funcotator - Inflater: IntelInflater
19:10:17.295 INFO  Funcotator - GCS max retries/reopens: 20
19:10:17.295 INFO  Funcotator - Requester pays: disabled
19:10:17.295 INFO  Funcotator - Initializing engine
19:10:17.297 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/vcfBugRepro.vcf
19:10:17.297 INFO  Funcotator - Done initializing engine
19:10:17.297 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:17.297 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:17.297 INFO  Funcotator - Initializing data sources...
19:10:17.297 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/
19:10:17.297 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:17.298 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
19:10:17.298 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
19:10:17.298 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
19:10:17.298 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:17.298 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
19:10:17.298 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
19:10:17.298 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
19:10:17.299 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
19:10:17.299 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
19:10:17.300 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
19:10:17.300 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:17.301 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
19:10:17.301 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
19:10:17.301 INFO  Funcotator - Initializing Funcotator Engine...
19:10:17.301 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:17.301 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.
19:10:17.301 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:17.301 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing2017217364927623723.vcf
19:10:17.302 INFO  ProgressMeter - Starting traversal
19:10:17.302 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:17.306 INFO  ProgressMeter -             unmapped              0.0                     1          15000.0
19:10:17.307 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
19:10:17.307 INFO  VcfFuncotationFactory - dbSnp fake cache hits/total: 0/1
19:10:17.309 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:17.309 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing2017217364927623723.vcf
19:10:17.396 INFO  Funcotator - ------------------------------------------------------------
19:10:17.396 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:17.396 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:17.396 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:17.396 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:17.396 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:17 PM GMT
19:10:17.396 INFO  Funcotator - ------------------------------------------------------------
19:10:17.396 INFO  Funcotator - ------------------------------------------------------------
19:10:17.396 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:17.396 INFO  Funcotator - Picard Version: 3.4.0
19:10:17.396 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:17.396 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:17.396 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:17.396 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:17.396 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:17.396 INFO  Funcotator - Deflater: IntelDeflater
19:10:17.396 INFO  Funcotator - Inflater: IntelInflater
19:10:17.396 INFO  Funcotator - GCS max retries/reopens: 20
19:10:17.396 INFO  Funcotator - Requester pays: disabled
19:10:17.396 INFO  Funcotator - Initializing engine
19:10:17.397 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
19:10:17.399 INFO  Funcotator - Done initializing engine
19:10:17.399 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:17.399 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:17.399 INFO  Funcotator - Initializing data sources...
19:10:17.399 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:17.399 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:17.399 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
19:10:17.399 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
19:10:17.399 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
19:10:17.399 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:17.399 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
19:10:17.399 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:17.400 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
19:10:17.400 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
19:10:17.400 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
19:10:17.400 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:17.401 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
19:10:17.401 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
19:10:17.402 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
19:10:17.403 INFO  Funcotator - Initializing Funcotator Engine...
19:10:17.403 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:17.403 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.
19:10:17.403 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out10661188276525587909.maf
19:10:17.404 INFO  ProgressMeter - Starting traversal
19:10:17.404 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:17.406 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.407 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.407 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.407 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.408 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.408 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.409 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.409 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.409 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.410 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.410 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.411 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.411 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.411 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.411 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.412 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.412 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.412 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.413 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.413 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.413 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:17.413 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
19:10:17.413 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
19:10:17.413 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
19:10:17.413 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:17.416 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
19:10:17.418 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
19:10:17.533 INFO  Funcotator - ------------------------------------------------------------
19:10:17.533 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:17.533 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:17.533 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:17.533 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:17.533 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:17 PM GMT
19:10:17.533 INFO  Funcotator - ------------------------------------------------------------
19:10:17.533 INFO  Funcotator - ------------------------------------------------------------
19:10:17.533 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:17.533 INFO  Funcotator - Picard Version: 3.4.0
19:10:17.533 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:17.533 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:17.533 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:17.533 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:17.533 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:17.533 INFO  Funcotator - Deflater: IntelDeflater
19:10:17.533 INFO  Funcotator - Inflater: IntelInflater
19:10:17.533 INFO  Funcotator - GCS max retries/reopens: 20
19:10:17.533 INFO  Funcotator - Requester pays: disabled
19:10:17.533 INFO  Funcotator - Initializing engine
19:10:17.534 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
19:10:17.535 INFO  Funcotator - Done initializing engine
19:10:17.535 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:17.535 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:17.535 INFO  Funcotator - Initializing data sources...
19:10:17.535 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:17.535 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:17.536 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
19:10:17.536 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
19:10:17.536 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
19:10:17.536 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:17.536 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
19:10:17.536 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:17.537 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
19:10:17.537 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
19:10:17.537 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
19:10:17.537 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:17.538 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
19:10:17.538 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
19:10:17.539 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
19:10:17.540 INFO  Funcotator - Initializing Funcotator Engine...
19:10:17.540 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:17.540 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.
19:10:17.540 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out16113826266571492141.vcf
19:10:17.543 INFO  ProgressMeter - Starting traversal
19:10:17.543 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:17.552 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
19:10:17.552 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
19:10:17.552 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
19:10:17.554 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:17.555 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out16113826266571492141.vcf
19:10:17.647 INFO  Funcotator - ------------------------------------------------------------
19:10:17.647 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:17.647 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:17.647 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:17.647 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:17.647 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:17 PM GMT
19:10:17.647 INFO  Funcotator - ------------------------------------------------------------
19:10:17.647 INFO  Funcotator - ------------------------------------------------------------
19:10:17.647 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:17.647 INFO  Funcotator - Picard Version: 3.4.0
19:10:17.647 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:17.647 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:17.647 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:17.647 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:17.647 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:17.647 INFO  Funcotator - Deflater: IntelDeflater
19:10:17.647 INFO  Funcotator - Inflater: IntelInflater
19:10:17.647 INFO  Funcotator - GCS max retries/reopens: 20
19:10:17.647 INFO  Funcotator - Requester pays: disabled
19:10:17.647 INFO  Funcotator - Initializing engine
19:10:17.648 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
19:10:17.649 INFO  Funcotator - Done initializing engine
19:10:17.649 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:17.649 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:17.649 INFO  Funcotator - Initializing data sources...
19:10:17.649 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:17.649 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:17.649 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
19:10:17.649 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
19:10:17.650 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
19:10:17.650 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:17.650 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
19:10:17.650 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:17.650 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
19:10:17.650 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
19:10:17.651 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
19:10:17.651 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:17.651 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
19:10:17.652 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
19:10:17.653 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
19:10:17.654 INFO  Funcotator - Initializing Funcotator Engine...
19:10:17.654 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:17.654 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.
19:10:17.654 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:17.654 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9806126310269668484.vcf
19:10:17.655 INFO  ProgressMeter - Starting traversal
19:10:17.655 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:17.659 INFO  ProgressMeter -             unmapped              0.0                     5          75000.0
19:10:17.659 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
19:10:17.659 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
19:10:17.662 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:17.662 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out9806126310269668484.vcf
19:10:17.757 INFO  Funcotator - ------------------------------------------------------------
19:10:17.757 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:17.757 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:17.757 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:17.757 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:17.757 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:17 PM GMT
19:10:17.757 INFO  Funcotator - ------------------------------------------------------------
19:10:17.757 INFO  Funcotator - ------------------------------------------------------------
19:10:17.757 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:17.757 INFO  Funcotator - Picard Version: 3.4.0
19:10:17.757 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:17.757 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:17.757 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:17.757 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:17.757 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:17.757 INFO  Funcotator - Deflater: IntelDeflater
19:10:17.757 INFO  Funcotator - Inflater: IntelInflater
19:10:17.757 INFO  Funcotator - GCS max retries/reopens: 20
19:10:17.757 INFO  Funcotator - Requester pays: disabled
19:10:17.757 INFO  Funcotator - Initializing engine
19:10:17.758 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
19:10:17.759 INFO  Funcotator - Done initializing engine
19:10:17.759 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:17.759 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:17.759 INFO  Funcotator - Initializing data sources...
19:10:17.759 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:17.759 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:17.759 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
19:10:17.759 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
19:10:17.759 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
19:10:17.759 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:17.759 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
19:10:17.759 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:17.760 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
19:10:17.760 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
19:10:17.760 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
19:10:17.760 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:17.761 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
19:10:17.762 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
19:10:17.763 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
19:10:17.763 INFO  Funcotator - Initializing Funcotator Engine...
19:10:17.764 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:17.764 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.
19:10:17.764 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:17.764 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out2467629317657749747.vcf
19:10:17.764 INFO  ProgressMeter - Starting traversal
19:10:17.764 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:17.774 INFO  ProgressMeter -             unmapped              0.0                    15          90000.0
19:10:17.774 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
19:10:17.774 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
19:10:17.777 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:17.860 INFO  Funcotator - ------------------------------------------------------------
19:10:17.860 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:17.860 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:17.860 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:17.860 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:17.861 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:17 PM GMT
19:10:17.861 INFO  Funcotator - ------------------------------------------------------------
19:10:17.861 INFO  Funcotator - ------------------------------------------------------------
19:10:17.861 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:17.861 INFO  Funcotator - Picard Version: 3.4.0
19:10:17.861 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:17.861 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:17.861 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:17.861 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:17.861 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:17.861 INFO  Funcotator - Deflater: IntelDeflater
19:10:17.861 INFO  Funcotator - Inflater: IntelInflater
19:10:17.861 INFO  Funcotator - GCS max retries/reopens: 20
19:10:17.861 INFO  Funcotator - Requester pays: disabled
19:10:17.861 INFO  Funcotator - Initializing engine
19:10:17.862 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
19:10:17.862 INFO  Funcotator - Done initializing engine
19:10:17.862 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:17.862 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:17.862 INFO  Funcotator - Initializing data sources...
19:10:17.862 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:17.862 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:17.862 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
19:10:17.862 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
19:10:17.862 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
19:10:17.863 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:17.863 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
19:10:17.863 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:17.863 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
19:10:17.863 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
19:10:17.864 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
19:10:17.864 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:17.864 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
19:10:17.865 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
19:10:17.866 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
19:10:17.867 INFO  Funcotator - Initializing Funcotator Engine...
19:10:17.867 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:17.867 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.
19:10:17.867 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:17.867 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out9215626208887548501.maf
19:10:17.867 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
19:10:17.867 INFO  ProgressMeter - Starting traversal
19:10:17.867 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:17.870 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 @ chr3:178916619 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
19:10:17.870 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 @ chr3:178916620 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
19:10:17.872 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 @ chr3:178916617 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
19:10:17.872 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 @ chr3:178919220 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
19:10:17.872 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 @ chr3:178921433 Q40.00 of type=SNP alleles=[A*, T] attr={} GT=[] filters=
19:10:17.873 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 @ chr3:178922366 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
19:10:17.873 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 @ chr3:178928317 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
19:10:17.873 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 @ chr3:178936091 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
19:10:17.874 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 @ chr3:178937063 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
19:10:17.874 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 @ chr3:178941890 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
19:10:17.874 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 @ chr3:178942511 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
19:10:17.875 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 @ chr3:178942523 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
19:10:17.875 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 @ chr3:178943785 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
19:10:17.875 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 @ chr3:178947158 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
19:10:17.876 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 @ chr3:178952085 Q40.00 of type=SNP alleles=[A*, T] attr={} GT=[] filters=
19:10:17.876 INFO  ProgressMeter -             unmapped              0.0                    15         100000.0
19:10:17.876 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
19:10:17.876 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
19:10:17.876 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:17.877 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out2467629317657749747.vcf
19:10:17.965 INFO  Funcotator - ------------------------------------------------------------
19:10:17.965 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:17.965 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:17.965 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:17.965 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:17.965 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:17 PM GMT
19:10:17.965 INFO  Funcotator - ------------------------------------------------------------
19:10:17.965 INFO  Funcotator - ------------------------------------------------------------
19:10:17.966 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:17.966 INFO  Funcotator - Picard Version: 3.4.0
19:10:17.966 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:17.966 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:17.966 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:17.966 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:17.966 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:17.966 INFO  Funcotator - Deflater: IntelDeflater
19:10:17.966 INFO  Funcotator - Inflater: IntelInflater
19:10:17.966 INFO  Funcotator - GCS max retries/reopens: 20
19:10:17.966 INFO  Funcotator - Requester pays: disabled
19:10:17.966 INFO  Funcotator - Initializing engine
19:10:17.967 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
19:10:17.967 INFO  Funcotator - Done initializing engine
19:10:17.967 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:17.967 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:17.967 INFO  Funcotator - Initializing data sources...
19:10:17.967 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:17.967 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:17.967 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
19:10:17.968 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
19:10:17.968 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
19:10:17.968 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:17.968 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
19:10:17.968 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:17.968 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
19:10:17.968 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
19:10:17.969 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
19:10:17.969 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:17.969 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
19:10:17.970 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
19:10:17.971 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
19:10:17.972 INFO  Funcotator - Initializing Funcotator Engine...
19:10:17.972 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:17.972 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.
19:10:17.972 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:17.972 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7092600551722641017.vcf
19:10:17.973 INFO  ProgressMeter - Starting traversal
19:10:17.973 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:18.012 INFO  ProgressMeter -             unmapped              0.0                    57          87692.3
19:10:18.012 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
19:10:18.012 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
19:10:18.014 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:18 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:18.102 INFO  Funcotator - ------------------------------------------------------------
19:10:18.102 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:18.103 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:18.103 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:18.103 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:18.103 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:18 PM GMT
19:10:18.103 INFO  Funcotator - ------------------------------------------------------------
19:10:18.103 INFO  Funcotator - ------------------------------------------------------------
19:10:18.103 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:18.103 INFO  Funcotator - Picard Version: 3.4.0
19:10:18.103 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:18.103 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:18.103 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:18.103 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:18.103 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:18.103 INFO  Funcotator - Deflater: IntelDeflater
19:10:18.103 INFO  Funcotator - Inflater: IntelInflater
19:10:18.103 INFO  Funcotator - GCS max retries/reopens: 20
19:10:18.103 INFO  Funcotator - Requester pays: disabled
19:10:18.103 INFO  Funcotator - Initializing engine
19:10:18.104 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
19:10:18.104 INFO  Funcotator - Done initializing engine
19:10:18.104 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:18.104 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:18.104 INFO  Funcotator - Initializing data sources...
19:10:18.104 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:18.104 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:18.104 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
19:10:18.104 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
19:10:18.105 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
19:10:18.105 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:18.105 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
19:10:18.105 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:18.105 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
19:10:18.106 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
19:10:18.106 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
19:10:18.106 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:18.106 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
19:10:18.107 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
19:10:18.108 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
19:10:18.110 INFO  Funcotator - Initializing Funcotator Engine...
19:10:18.110 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:18.110 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.
19:10:18.110 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:18.110 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out715632431839591651.maf
19:10:18.110 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
19:10:18.110 INFO  ProgressMeter - Starting traversal
19:10:18.110 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:18.114 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCGA] attr={} GT=[] filters=
19:10:18.114 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGAG] attr={} GT=[] filters=
19:10:18.115 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165 Q40.00 of type=INDEL alleles=[G*, GT] attr={} GT=[] filters=
19:10:18.115 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
19:10:18.116 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCG] attr={} GT=[] filters=
19:10:18.116 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGA] attr={} GT=[] filters=
19:10:18.117 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 @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
19:10:18.117 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 @ chr3:178948154 Q40.00 of type=INDEL alleles=[G*, GGAATT] attr={} GT=[] filters=
19:10:18.118 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
19:10:18.118 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
19:10:18.118 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948157 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
19:10:18.118 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948158 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
19:10:18.119 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, ATGA] attr={} GT=[] filters=
19:10:18.120 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916937-178916940 Q40.00 of type=INDEL alleles=[TGAA*, T] attr={} GT=[] filters=
19:10:18.120 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948162 Q40.00 of type=INDEL alleles=[TGAG*, T] attr={} GT=[] filters=
19:10:18.121 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948161 Q40.00 of type=INDEL alleles=[TGA*, T] attr={} GT=[] filters=
19:10:18.121 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948158 Q40.00 of type=INDEL alleles=[AGAATT*, A] attr={} GT=[] filters=
19:10:18.122 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 @ chr3:178948153-178948157 Q40.00 of type=INDEL alleles=[AGAAT*, A] attr={} GT=[] filters=
19:10:18.122 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 @ chr3:178948159-178948164 Q40.00 of type=INDEL alleles=[TGAGAG*, T] attr={} GT=[] filters=
19:10:18.122 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 @ chr3:178948165-178948168 Q40.00 of type=INDEL alleles=[GTGA*, G] attr={} GT=[] filters=
19:10:18.123 WARN  MafOutputRenderer - 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=
19:10:18.124 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 @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATAT] attr={} GT=[] filters=
19:10:18.125 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTAT] attr={} GT=[] filters=
19:10:18.125 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 @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
19:10:18.125 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 @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ACTTGAAGAA] attr={} GT=[] filters=
19:10:18.127 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 @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
19:10:18.127 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 @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATA] attr={} GT=[] filters=
19:10:18.128 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTA] attr={} GT=[] filters=
19:10:18.128 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 @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
19:10:18.129 WARN  MafOutputRenderer - 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=
19:10:18.129 WARN  MafOutputRenderer - 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=
19:10:18.130 WARN  MafOutputRenderer - 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=
19:10:18.130 WARN  MafOutputRenderer - 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=
19:10:18.131 WARN  MafOutputRenderer - 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=
19:10:18.131 WARN  MafOutputRenderer - 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=
19:10:18.132 WARN  MafOutputRenderer - 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=
19:10:18.132 WARN  MafOutputRenderer - 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=
19:10:18.134 WARN  MafOutputRenderer - 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=
19:10:18.134 WARN  MafOutputRenderer - 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=
19:10:18.134 WARN  MafOutputRenderer - 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=
19:10:18.134 WARN  MafOutputRenderer - 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=
19:10:18.136 WARN  MafOutputRenderer - 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=
19:10:18.136 WARN  MafOutputRenderer - 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=
19:10:18.136 WARN  MafOutputRenderer - 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=
19:10:18.136 WARN  MafOutputRenderer - 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=
19:10:18.138 WARN  MafOutputRenderer - 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=
19:10:18.138 WARN  MafOutputRenderer - 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=
19:10:18.138 WARN  MafOutputRenderer - 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=
19:10:18.138 WARN  MafOutputRenderer - 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=
19:10:18.140 WARN  MafOutputRenderer - 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=
19:10:18.140 WARN  MafOutputRenderer - 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=
19:10:18.141 WARN  MafOutputRenderer - 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=
19:10:18.141 WARN  MafOutputRenderer - 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=
19:10:18.142 WARN  MafOutputRenderer - 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=
19:10:18.142 WARN  MafOutputRenderer - 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=
19:10:18.143 WARN  MafOutputRenderer - 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=
19:10:18.143 WARN  MafOutputRenderer - 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=
19:10:18.143 INFO  ProgressMeter -             unmapped              0.0                    57         103636.4
19:10:18.143 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
19:10:18.143 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
19:10:18.143 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:18 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:18.144 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7092600551722641017.vcf
19:10:18.247 INFO  Funcotator - ------------------------------------------------------------
19:10:18.247 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:18.247 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:18.247 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:18.247 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:18.247 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:18 PM GMT
19:10:18.247 INFO  Funcotator - ------------------------------------------------------------
19:10:18.247 INFO  Funcotator - ------------------------------------------------------------
19:10:18.248 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:18.248 INFO  Funcotator - Picard Version: 3.4.0
19:10:18.248 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:18.248 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:18.248 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:18.248 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:18.248 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:18.248 INFO  Funcotator - Deflater: IntelDeflater
19:10:18.248 INFO  Funcotator - Inflater: IntelInflater
19:10:18.248 INFO  Funcotator - GCS max retries/reopens: 20
19:10:18.248 INFO  Funcotator - Requester pays: disabled
19:10:18.248 INFO  Funcotator - Initializing engine
19:10:18.249 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
19:10:18.249 INFO  Funcotator - Done initializing engine
19:10:18.249 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:18.249 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:18.249 INFO  Funcotator - Initializing data sources...
19:10:18.249 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:18.249 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:18.250 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
19:10:18.250 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
19:10:18.250 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
19:10:18.250 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
19:10:18.250 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
19:10:18.251 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
19:10:18.251 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
19:10:18.251 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:18.251 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
19:10:18.251 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
19:10:18.251 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
19:10:18.251 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
19:10:18.252 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:18.252 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
19:10:18.252 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
19:10:18.252 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:18.252 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
19:10:18.252 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
19:10:18.271 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
19:10:18.272 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
19:10:18.333 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
19:10:18.333 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
19:10:18.866 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:18.866 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:18.867 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:18.869 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:18.871 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:18.873 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:18.873 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:18.874 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:18.900 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:18.900 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-19 19:10:18	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:18.901 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
19:10:18.938 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
19:10:18.938 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
19:10:18.939 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
19:10:18.947 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:18.947 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
19:10:18.947 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:18.948 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:18.948 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
19:10:19.025 INFO  Funcotator - Initializing Funcotator Engine...
19:10:19.025 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:19.025 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:19.025 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4100902535735670706.vcf
19:10:19.026 INFO  ProgressMeter - Starting traversal
19:10:19.026 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:34.515 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7747.4
19:10:34.977 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)
19:10:34.978 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)
19:10:35.705 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7399.7
19:10:35.705 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
19:10:35.705 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
19:10:35.707 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:35 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.29 minutes.
Runtime.totalMemory()=2887778304
19:10:35.807 INFO  Funcotator - ------------------------------------------------------------
19:10:35.807 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:35.807 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:35.807 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:35.807 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:35.807 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:35 PM GMT
19:10:35.807 INFO  Funcotator - ------------------------------------------------------------
19:10:35.807 INFO  Funcotator - ------------------------------------------------------------
19:10:35.808 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:35.808 INFO  Funcotator - Picard Version: 3.4.0
19:10:35.808 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:35.808 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:35.808 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:35.808 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:35.808 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:35.808 INFO  Funcotator - Deflater: IntelDeflater
19:10:35.808 INFO  Funcotator - Inflater: IntelInflater
19:10:35.808 INFO  Funcotator - GCS max retries/reopens: 20
19:10:35.808 INFO  Funcotator - Requester pays: disabled
19:10:35.808 INFO  Funcotator - Initializing engine
19:10:35.809 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
19:10:35.809 INFO  Funcotator - Done initializing engine
19:10:35.809 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:35.809 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:35.809 INFO  Funcotator - Initializing data sources...
19:10:35.809 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
19:10:35.809 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:35.809 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
19:10:35.810 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
19:10:35.810 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
19:10:35.810 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
19:10:35.810 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
19:10:35.810 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
19:10:35.810 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
19:10:35.811 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:35.811 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
19:10:35.811 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
19:10:35.811 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
19:10:35.811 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
19:10:35.811 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:35.812 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
19:10:35.812 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
19:10:35.812 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:35.812 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
19:10:35.812 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
19:10:35.831 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
19:10:35.832 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
19:10:35.877 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
19:10:35.878 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
19:10:36.441 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
19:10:36.441 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
19:10:36.442 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:36.444 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
19:10:36.447 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
19:10:36.449 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:36.449 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:36.449 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
19:10:36.476 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
19:10:36.476 INFO  DataSourceUtils - 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	2025-05-19 19:10:36	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:36.476 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
19:10:36.513 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
19:10:36.514 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
19:10:36.514 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
19:10:36.522 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
19:10:36.523 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
19:10:36.523 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:36.523 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
19:10:36.524 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
19:10:36.599 INFO  Funcotator - Initializing Funcotator Engine...
19:10:36.599 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:36.599 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:36.599 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out16506710239189058720.maf
19:10:36.599 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
19:10:36.600 INFO  ProgressMeter - Starting traversal
19:10:36.600 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:52.085 INFO  ProgressMeter -        chr19:9077594              0.3                  2000           7749.4
19:10:52.559 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)
19:10:52.560 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)
19:10:53.287 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7396.2
19:10:53.287 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
19:10:53.287 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
19:10:53.288 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:53 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.29 minutes.
Runtime.totalMemory()=2887778304
19:10:53.289 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4100902535735670706.vcf
19:10:53.693 INFO  Funcotator - ------------------------------------------------------------
19:10:53.693 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:53.693 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:53.693 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:53.693 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:53.693 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:53 PM GMT
19:10:53.693 INFO  Funcotator - ------------------------------------------------------------
19:10:53.693 INFO  Funcotator - ------------------------------------------------------------
19:10:53.693 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:53.693 INFO  Funcotator - Picard Version: 3.4.0
19:10:53.693 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:53.693 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:53.693 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:53.693 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:53.693 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:53.693 INFO  Funcotator - Deflater: IntelDeflater
19:10:53.693 INFO  Funcotator - Inflater: IntelInflater
19:10:53.693 INFO  Funcotator - GCS max retries/reopens: 20
19:10:53.693 INFO  Funcotator - Requester pays: disabled
19:10:53.693 INFO  Funcotator - Initializing engine
19:10:53.694 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
19:10:53.710 INFO  Funcotator - Done initializing engine
19:10:53.710 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:53.710 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:53.710 INFO  Funcotator - Initializing data sources...
19:10:53.710 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:53.710 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:53.711 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
19:10:53.711 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
19:10:53.711 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
19:10:53.711 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:53.711 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
19:10:53.711 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:53.712 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
19:10:53.712 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
19:10:53.712 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
19:10:53.712 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:53.713 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
19:10:53.720 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
19:10:53.729 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
19:10:53.737 INFO  Funcotator - Initializing Funcotator Engine...
19:10:53.744 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:53.744 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out18178085107798182528.vcf
19:10:53.755 INFO  ProgressMeter - Starting traversal
19:10:53.755 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:53.778 INFO  ProgressMeter -             unmapped              0.0                   100         260869.6
19:10:53.778 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
19:10:53.778 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
19:10:53.783 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:53 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:53.870 INFO  Funcotator - ------------------------------------------------------------
19:10:53.870 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:53.870 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:53.870 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:53.870 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:53.870 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:53 PM GMT
19:10:53.870 INFO  Funcotator - ------------------------------------------------------------
19:10:53.870 INFO  Funcotator - ------------------------------------------------------------
19:10:53.870 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:53.870 INFO  Funcotator - Picard Version: 3.4.0
19:10:53.870 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:53.870 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:53.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:53.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:53.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:53.870 INFO  Funcotator - Deflater: IntelDeflater
19:10:53.870 INFO  Funcotator - Inflater: IntelInflater
19:10:53.870 INFO  Funcotator - GCS max retries/reopens: 20
19:10:53.870 INFO  Funcotator - Requester pays: disabled
19:10:53.870 INFO  Funcotator - Initializing engine
19:10:53.871 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
19:10:53.887 INFO  Funcotator - Done initializing engine
19:10:53.887 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:53.887 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:53.887 INFO  Funcotator - Initializing data sources...
19:10:53.887 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:53.887 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:53.888 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
19:10:53.888 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
19:10:53.888 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
19:10:53.888 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:53.888 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
19:10:53.888 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:53.889 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
19:10:53.889 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
19:10:53.889 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
19:10:53.889 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:53.890 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
19:10:53.897 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
19:10:53.906 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
19:10:53.913 INFO  Funcotator - Initializing Funcotator Engine...
19:10:53.918 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
19:10:53.918 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8846770682962216396.maf
19:10:53.918 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
19:10:53.919 INFO  ProgressMeter - Starting traversal
19:10:53.919 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:53.921 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179126640-179126641 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=
19:10:53.926 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179127567 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=
19:10:53.926 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179128974 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+
19:10:53.926 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179129966 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+
19:10:53.926 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179130674 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+
19:10:53.927 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179134890 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+
19:10:53.927 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179135392-179135396 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=
19:10:53.927 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179139036 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=
19:10:53.927 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179140609 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=
19:10:53.927 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179143781 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=
19:10:53.928 WARN  MafOutputRenderer - 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=
19:10:53.928 WARN  MafOutputRenderer - 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=
19:10:53.928 WARN  MafOutputRenderer - 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=
19:10:53.929 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179153825-179153826 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=
19:10:53.929 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179162859 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=
19:10:53.929 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179163705 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=
19:10:53.929 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179170066 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=
19:10:53.929 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179170076 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=
19:10:53.930 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179172828 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=
19:10:53.930 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179173402 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+
19:10:53.930 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179173404 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
19:10:53.931 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179177312-179177313 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=
19:10:53.931 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179178119-179178120 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=
19:10:53.931 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179184000-179184003 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=
19:10:53.931 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179187736 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=
19:10:53.932 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179190789 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=
19:10:53.932 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179190993 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=
19:10:53.932 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179192974 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=
19:10:53.932 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179201626 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
19:10:53.933 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179204486 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=
19:10:53.933 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179205020-179205028 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=
19:10:53.933 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179206086-179206087 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=
19:10:53.933 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179207079 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=
19:10:53.933 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179207762 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=
19:10:53.934 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179215394 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=
19:10:53.934 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179215575 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=
19:10:53.934 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179217522 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=
19:10:53.934 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179221303 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=
19:10:53.934 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179221696 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=
19:10:53.935 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179224643 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=
19:10:53.935 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179226199 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=
19:10:53.936 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179231630 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=
19:10:53.936 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179232352 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=
19:10:53.936 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179232509 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=
19:10:53.937 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179236244-179236250 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=
19:10:53.937 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179242400-179242401 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=
19:10:53.937 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179243192 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+
19:10:53.937 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179244582 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=
19:10:53.938 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179244703 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=
19:10:53.938 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179246281 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=
19:10:53.938 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179247445 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=
19:10:53.938 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179249007 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=
19:10:53.938 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179249792 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=
19:10:53.939 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 @ chr3:179249918 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=
19:10:53.939 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 @ chr3:179250038 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=
19:10:53.939 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 @ chr3:179250846 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=
19:10:53.939 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 @ chr3:179250872 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=
19:10:53.939 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 @ chr3:179251319 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=
19:10:53.939 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 @ chr3:179251568-179251569 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=
19:10:53.940 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 @ chr3:179251754 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=
19:10:53.940 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 @ chr3:179251923 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=
19:10:53.940 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 @ chr3:179251953 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=
19:10:53.940 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 @ chr3:179252222 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=
19:10:53.940 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 @ chr3:179253641 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=
19:10:53.941 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 @ chr3:179253762 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=
19:10:53.941 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 @ chr3:179255161 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=
19:10:53.941 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 @ chr3:179255164 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=
19:10:53.941 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 @ chr3:179255188 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=
19:10:53.941 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 @ chr3:179255255 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=
19:10:53.942 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 @ chr3:179255327 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=
19:10:53.942 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 @ chr3:179255934 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=
19:10:53.942 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 @ chr3:179256242 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=
19:10:53.942 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 @ chr3:179256462 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=
19:10:53.942 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 @ chr3:179256883 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=
19:10:53.943 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 @ chr3:179257051 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=
19:10:53.943 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 @ chr3:179257184 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=
19:10:53.943 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 @ chr3:179257620 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=
19:10:53.943 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 @ chr3:179257738 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=
19:10:53.943 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 @ chr3:179257767 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=
19:10:53.944 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 @ chr3:179257889-179257890 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=
19:10:53.944 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 @ chr3:179257891-179257898 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=
19:10:53.944 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 @ chr3:179258111 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=
19:10:53.944 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 @ chr3:179258178 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=
19:10:53.944 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 @ chr3:179258390 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=
19:10:53.944 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 @ chr3:179258419 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=
19:10:53.945 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 @ chr3:179258803 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=
19:10:53.945 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 @ chr3:179258989 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=
19:10:53.945 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 @ chr3:179259033 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=
19:10:53.945 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 @ chr3:179259323 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=
19:10:53.945 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 @ chr3:179260056 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=
19:10:53.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260290 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=
19:10:53.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260540 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=
19:10:53.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260754 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=
19:10:53.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260816 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=
19:10:53.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179260901 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=
19:10:53.947 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 @ chr3:179260930 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=
19:10:53.947 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 @ chr3:179262286 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=
19:10:53.947 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 @ chr3:179262480 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=
19:10:53.947 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 @ chr3:179262545 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=
19:10:53.947 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 @ chr3:179262851 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=
19:10:53.948 INFO  ProgressMeter -             unmapped              0.0                   100         206896.6
19:10:53.948 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
19:10:53.948 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
19:10:53.948 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:53 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:53.949 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out18178085107798182528.vcf
19:10:54.098 INFO  Funcotator - ------------------------------------------------------------
19:10:54.098 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:54.098 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:54.098 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:54.098 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:54.098 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:54 PM GMT
19:10:54.098 INFO  Funcotator - ------------------------------------------------------------
19:10:54.098 INFO  Funcotator - ------------------------------------------------------------
19:10:54.098 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:54.098 INFO  Funcotator - Picard Version: 3.4.0
19:10:54.098 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:54.098 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:54.098 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:54.098 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:54.098 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:54.098 INFO  Funcotator - Deflater: IntelDeflater
19:10:54.098 INFO  Funcotator - Inflater: IntelInflater
19:10:54.098 INFO  Funcotator - GCS max retries/reopens: 20
19:10:54.098 INFO  Funcotator - Requester pays: disabled
19:10:54.098 INFO  Funcotator - Initializing engine
19:10:54.099 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
19:10:54.100 INFO  Funcotator - Done initializing engine
19:10:54.100 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:54.100 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:54.100 INFO  Funcotator - Initializing data sources...
19:10:54.100 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:54.100 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:54.100 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
19:10:54.100 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
19:10:54.100 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
19:10:54.100 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:54.100 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
19:10:54.100 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:54.101 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
19:10:54.101 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
19:10:54.101 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
19:10:54.101 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:54.102 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
19:10:54.103 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
19:10:54.104 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
19:10:54.105 INFO  Funcotator - Initializing Funcotator Engine...
19:10:54.105 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:54.105 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.
19:10:54.105 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:54.105 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3890505375196125952.vcf
19:10:54.105 INFO  ProgressMeter - Starting traversal
19:10:54.105 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:54.137 INFO  ProgressMeter -             unmapped              0.0                    57         106875.0
19:10:54.137 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
19:10:54.137 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
19:10:54.139 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:54 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:54.230 INFO  Funcotator - ------------------------------------------------------------
19:10:54.230 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:54.230 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:54.230 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:54.230 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:54.230 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:54 PM GMT
19:10:54.230 INFO  Funcotator - ------------------------------------------------------------
19:10:54.230 INFO  Funcotator - ------------------------------------------------------------
19:10:54.230 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:54.230 INFO  Funcotator - Picard Version: 3.4.0
19:10:54.230 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:54.230 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:54.230 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:54.230 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:54.230 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:54.230 INFO  Funcotator - Deflater: IntelDeflater
19:10:54.230 INFO  Funcotator - Inflater: IntelInflater
19:10:54.230 INFO  Funcotator - GCS max retries/reopens: 20
19:10:54.230 INFO  Funcotator - Requester pays: disabled
19:10:54.230 INFO  Funcotator - Initializing engine
19:10:54.231 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
19:10:54.232 INFO  Funcotator - Done initializing engine
19:10:54.232 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:54.232 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:54.232 INFO  Funcotator - Initializing data sources...
19:10:54.232 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:54.232 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:54.232 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
19:10:54.232 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
19:10:54.232 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
19:10:54.232 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:54.232 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
19:10:54.232 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:54.233 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
19:10:54.233 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
19:10:54.233 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
19:10:54.233 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:54.234 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
19:10:54.234 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
19:10:54.235 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
19:10:54.236 INFO  Funcotator - Initializing Funcotator Engine...
19:10:54.236 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:54.236 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.
19:10:54.236 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
19:10:54.236 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out8620230444370860712.maf
19:10:54.236 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
19:10:54.236 INFO  ProgressMeter - Starting traversal
19:10:54.237 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:54.239 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCGA] attr={} GT=[] filters=
19:10:54.239 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 @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGAG] attr={} GT=[] filters=
19:10:54.239 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 @ chr3:178948165 Q40.00 of type=INDEL alleles=[G*, GT] attr={} GT=[] filters=
19:10:54.240 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 @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
19:10:54.241 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 @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCG] attr={} GT=[] filters=
19:10:54.241 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 @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGA] attr={} GT=[] filters=
19:10:54.242 WARN  MafOutputRenderer - 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=
19:10:54.242 WARN  MafOutputRenderer - 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=
19:10:54.243 WARN  MafOutputRenderer - 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=
19:10:54.243 WARN  MafOutputRenderer - 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=
19:10:54.243 WARN  MafOutputRenderer - 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=
19:10:54.244 WARN  MafOutputRenderer - 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=
19:10:54.244 WARN  MafOutputRenderer - 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=
19:10:54.246 WARN  MafOutputRenderer - 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=
19:10:54.247 WARN  MafOutputRenderer - 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=
19:10:54.247 WARN  MafOutputRenderer - 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=
19:10:54.249 WARN  MafOutputRenderer - 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=
19:10:54.249 WARN  MafOutputRenderer - 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=
19:10:54.250 WARN  MafOutputRenderer - 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=
19:10:54.250 WARN  MafOutputRenderer - 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=
19:10:54.252 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
19:10:54.252 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATAT] attr={} GT=[] filters=
19:10:54.255 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTAT] attr={} GT=[] filters=
19:10:54.255 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
19:10:54.256 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ACTTGAAGAA] attr={} GT=[] filters=
19:10:54.258 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
19:10:54.258 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATA] attr={} GT=[] filters=
19:10:54.260 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTA] attr={} GT=[] filters=
19:10:54.261 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
19:10:54.261 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
19:10:54.262 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
19:10:54.264 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
19:10:54.264 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
19:10:54.265 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
19:10:54.265 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATATT] attr={} GT=[] filters=
19:10:54.267 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
19:10:54.267 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
19:10:54.269 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916621 Q40.00 of type=INDEL alleles=[CTCC*, C] attr={} GT=[] filters=
19:10:54.270 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916622 Q40.00 of type=INDEL alleles=[TCCA*, T] attr={} GT=[] filters=
19:10:54.270 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916623 Q40.00 of type=INDEL alleles=[CCAC*, C] attr={} GT=[] filters=
19:10:54.271 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916624 Q40.00 of type=INDEL alleles=[CACG*, C] attr={} GT=[] filters=
19:10:54.273 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916620 Q40.00 of type=INDEL alleles=[CTC*, C] attr={} GT=[] filters=
19:10:54.273 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916621 Q40.00 of type=INDEL alleles=[TCC*, T] attr={} GT=[] filters=
19:10:54.274 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916622 Q40.00 of type=INDEL alleles=[CCA*, C] attr={} GT=[] filters=
19:10:54.274 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916623 Q40.00 of type=INDEL alleles=[CAC*, C] attr={} GT=[] filters=
19:10:54.276 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916619 Q40.00 of type=INDEL alleles=[CT*, C] attr={} GT=[] filters=
19:10:54.277 WARN  MafOutputRenderer - 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=
19:10:54.277 WARN  MafOutputRenderer - 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=
19:10:54.278 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
19:10:54.280 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916622 Q40.00 of type=INDEL alleles=[CTCCA*, C] attr={} GT=[] filters=
19:10:54.280 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916623 Q40.00 of type=INDEL alleles=[TCCAC*, T] attr={} GT=[] filters=
19:10:54.281 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916624 Q40.00 of type=INDEL alleles=[CCACG*, C] attr={} GT=[] filters=
19:10:54.281 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916625 Q40.00 of type=INDEL alleles=[CACGA*, C] attr={} GT=[] filters=
19:10:54.283 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916625 Q40.00 of type=INDEL alleles=[CTCCACGA*, C] attr={} GT=[] filters=
19:10:54.284 WARN  MafOutputRenderer - 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=
19:10:54.284 WARN  MafOutputRenderer - 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=
19:10:54.284 WARN  MafOutputRenderer - 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=
19:10:54.285 INFO  ProgressMeter -             unmapped              0.0                    57          71250.0
19:10:54.285 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
19:10:54.285 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
19:10:54.285 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:54 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:54.286 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3890505375196125952.vcf
19:10:54.406 INFO  Funcotator - ------------------------------------------------------------
19:10:54.406 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:54.406 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:54.406 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:54.406 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:54.406 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:54 PM GMT
19:10:54.406 INFO  Funcotator - ------------------------------------------------------------
19:10:54.406 INFO  Funcotator - ------------------------------------------------------------
19:10:54.406 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:54.406 INFO  Funcotator - Picard Version: 3.4.0
19:10:54.406 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:54.406 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:54.406 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:54.406 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:54.406 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:54.406 INFO  Funcotator - Deflater: IntelDeflater
19:10:54.406 INFO  Funcotator - Inflater: IntelInflater
19:10:54.406 INFO  Funcotator - GCS max retries/reopens: 20
19:10:54.406 INFO  Funcotator - Requester pays: disabled
19:10:54.406 INFO  Funcotator - Initializing engine
19:10:54.407 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
19:10:54.408 INFO  Funcotator - Done initializing engine
19:10:54.408 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:54.408 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:54.408 INFO  Funcotator - Initializing data sources...
19:10:54.408 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
19:10:54.408 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:54.408 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
19:10:54.408 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
19:10:54.408 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
19:10:54.408 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:54.409 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
19:10:54.409 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:54.409 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
19:10:54.409 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
19:10:54.410 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
19:10:54.410 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
19:10:54.410 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
19:10:54.411 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
19:10:54.412 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
19:10:54.413 INFO  Funcotator - Initializing Funcotator Engine...
19:10:54.413 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:54.413 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
19:10:54.413 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out9534994846974082284.maf
19:10:54.414 INFO  ProgressMeter - Starting traversal
19:10:54.414 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:54.416 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:54.417 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:54.417 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:54.418 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:54.418 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:54.418 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
19:10:54.419 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178922361 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=
19:10:54.419 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178927410 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=
19:10:54.420 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178932551 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=
19:10:54.420 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178937400 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=
19:10:54.420 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178947118 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=
19:10:54.421 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178950297 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=
19:10:54.421 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960744 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=
19:10:54.421 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178960843 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=
19:10:54.421 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962380 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=
19:10:54.422 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178962425 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=
19:10:54.422 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968543 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=
19:10:54.422 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968568 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=
19:10:54.423 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968634 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=
19:10:54.423 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968660 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=
19:10:54.423 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178968848 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=
19:10:54.423 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
19:10:54.423 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
19:10:54.423 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
19:10:54.423 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:54 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:54.516 INFO  Funcotator - ------------------------------------------------------------
19:10:54.516 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:54.516 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:54.516 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:54.516 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:54.516 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:54 PM GMT
19:10:54.516 INFO  Funcotator - ------------------------------------------------------------
19:10:54.516 INFO  Funcotator - ------------------------------------------------------------
19:10:54.516 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:54.516 INFO  Funcotator - Picard Version: 3.4.0
19:10:54.516 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:54.516 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:54.516 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:54.516 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:54.516 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:54.516 INFO  Funcotator - Deflater: IntelDeflater
19:10:54.516 INFO  Funcotator - Inflater: IntelInflater
19:10:54.516 INFO  Funcotator - GCS max retries/reopens: 20
19:10:54.516 INFO  Funcotator - Requester pays: disabled
19:10:54.516 INFO  Funcotator - Initializing engine
19:10:54.517 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
19:10:54.518 INFO  Funcotator - Done initializing engine
19:10:54.518 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:54.518 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:54.518 INFO  Funcotator - Initializing data sources...
19:10:54.518 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
19:10:54.518 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:54.518 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
19:10:54.519 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
19:10:54.519 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
19:10:54.519 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:54.519 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:54.519 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
19:10:54.520 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
19:10:54.546 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
19:10:54.546 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	2025-05-19 19:10:54	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:54.546 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
19:10:54.546 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:54.548 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
19:10:54.548 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
19:10:54.548 INFO  Funcotator - Initializing Funcotator Engine...
19:10:54.548 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:54.549 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.
19:10:54.549 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out15463537088589259343.vcf
19:10:54.554 INFO  ProgressMeter - Starting traversal
19:10:54.554 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:54.560 INFO  ProgressMeter -             unmapped              0.0                    10         100000.0
19:10:54.560 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
19:10:54.560 WARN  Funcotator - ================================================================================
19:10:54.560 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
19:10:54.560 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
19:10:54.560 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
19:10:54.560 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
19:10:54.560 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
19:10:54.560 WARN  Funcotator -                                                   |___/                         ?[0;0m
19:10:54.560 WARN  Funcotator - --------------------------------------------------------------------------------
19:10:54.560 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
19:10:54.560 WARN  Funcotator -  run was misconfigured.     
19:10:54.560 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
19:10:54.560 WARN  Funcotator - ================================================================================
19:10:54.560 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:54 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:54.561 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out15463537088589259343.vcf
19:10:54.650 INFO  Funcotator - ------------------------------------------------------------
19:10:54.650 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:10:54.650 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:54.650 INFO  Funcotator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:10:54.650 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:10:54.650 INFO  Funcotator - Start Date/Time: May 19, 2025 at 7:10:54 PM GMT
19:10:54.650 INFO  Funcotator - ------------------------------------------------------------
19:10:54.650 INFO  Funcotator - ------------------------------------------------------------
19:10:54.650 INFO  Funcotator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:10:54.650 INFO  Funcotator - Picard Version: 3.4.0
19:10:54.651 INFO  Funcotator - Built for Spark Version: 3.5.0
19:10:54.651 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:54.651 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:54.651 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:54.651 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:54.651 INFO  Funcotator - Deflater: IntelDeflater
19:10:54.651 INFO  Funcotator - Inflater: IntelInflater
19:10:54.651 INFO  Funcotator - GCS max retries/reopens: 20
19:10:54.651 INFO  Funcotator - Requester pays: disabled
19:10:54.651 INFO  Funcotator - Initializing engine
19:10:54.652 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_multihit_test.vcf
19:10:54.653 INFO  Funcotator - Done initializing engine
19:10:54.653 INFO  Funcotator - Skipping sequence dictionary validation.
19:10:54.653 INFO  Funcotator - Processing user transcripts/defaults/overrides...
19:10:54.653 INFO  Funcotator - Initializing data sources...
19:10:54.653 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
19:10:54.653 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
19:10:54.653 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
19:10:54.653 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
19:10:54.653 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
19:10:54.653 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
19:10:54.653 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
19:10:54.654 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
19:10:54.654 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
19:10:54.681 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
19:10:54.681 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	2025-05-19 19:10:54	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:10:54.681 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
19:10:54.681 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
19:10:54.682 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
19:10:54.682 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
19:10:54.682 INFO  Funcotator - Initializing Funcotator Engine...
19:10:54.683 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
19:10:54.683 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.
19:10:54.683 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out792412697338845216.vcf
19:10:54.686 INFO  ProgressMeter - Starting traversal
19:10:54.686 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:10:54.687 INFO  ProgressMeter -             unmapped              0.0                     1          60000.0
19:10:54.687 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
19:10:54.687 WARN  Funcotator - ================================================================================
19:10:54.687 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
19:10:54.687 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
19:10:54.687 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
19:10:54.687 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
19:10:54.687 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
19:10:54.687 WARN  Funcotator -                                                   |___/                         ?[0;0m
19:10:54.687 WARN  Funcotator - --------------------------------------------------------------------------------
19:10:54.687 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
19:10:54.687 WARN  Funcotator -  run was misconfigured.     
19:10:54.687 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
19:10:54.687 WARN  Funcotator - ================================================================================
19:10:54.688 INFO  Funcotator - Shutting down engine
[May 19, 2025 at 7:10:54 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2887778304
19:10:54.689 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out792412697338845216.vcf