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

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

tests
0

failures
0

ignored
1m37.70s

duration
100%

successful

Tests

Test Duration Result
exhaustiveArgumentTest[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder18432782024826549230/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null) 1.090s passed
exhaustiveArgumentTest[1](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder460415242273313878/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null) 1.155s passed
exhaustiveArgumentTest[2](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder18432782024826549230/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null) 1.048s passed
exhaustiveArgumentTest[3](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder460415242273313878/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null) 1.148s passed
exhaustiveArgumentTest[4](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder18432782024826549230/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null) 1.119s passed
exhaustiveArgumentTest[5](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder460415242273313878/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null) 1.150s passed
exhaustiveArgumentTest[6](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder18432782024826549230/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null) 1.109s passed
exhaustiveArgumentTest[7](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder460415242273313878/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null) 1.104s 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) 6.152s 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) 5.361s passed
nonTrivialLargeDataValidationTest[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf, [], false) 2.003s passed
nonTrivialLargeDataValidationTest[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz, hg38, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf, [], false) 1.881s 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) 12.233s 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) 5.742s 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) 0.098s passed
testCanAnnotateHg38ClinvarAndGencodeV28 0.209s passed
testCanAnnotateMixedContigHg19Clinvar 0.123s passed
testCanAnnotateSpanningDeletions 0.186s passed
testCanCreateNonLocatableFuncotations 0.970s passed
testCanHandleSymbollicAlleleFuncotations 0.952s passed
testCustomVariantClassificationOrder 0.941s passed
testEColiFuncotations 0.128s passed
testEnsureDbSnpInMaf 0.099s passed
testExclusionFromDatasourceVcfToVcf 0.204s passed
testFilterParsing 0.135s passed
testFuncotatorWithoutValidatingResults[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder18432782024826549230/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null) 0.924s passed
testFuncotatorWithoutValidatingResults[1](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder460415242273313878/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null) 1.011s passed
testFuncotatorWithoutValidatingResults[2](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder18432782024826549230/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null) 0.943s passed
testFuncotatorWithoutValidatingResults[3](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder460415242273313878/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null) 1.017s passed
testFuncotatorWithoutValidatingResults[4](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder18432782024826549230/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null) 0.913s passed
testFuncotatorWithoutValidatingResults[5](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder460415242273313878/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null) 1.013s passed
testFuncotatorWithoutValidatingResults[6](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder18432782024826549230/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null) 0.894s passed
testFuncotatorWithoutValidatingResults[7](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder460415242273313878/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null) 0.972s passed
testMANESelectAnnotationDifferencesAndGencodeV43 0.379s passed
testMafCustomCountFieldsTumorOnly[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf) 0.107s passed
testMafCustomCountFieldsTumorOnly[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields_tumor_only.vcf) 0.106s passed
testMafCustomCountFields[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf) 0.123s passed
testMafCustomCountFields[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf) 0.109s passed
testManualAnnotationsCorrectness 0.122s passed
testMoreThanOneTNPair 0.101s passed
testNoSpanningDeletionWriteWithMAF 0.152s passed
testNoVariantsProduceMaf 0.099s passed
testSequenceDictionaryCheck 0.093s passed
testUnannotatedInputWithOverrideArgument[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf) 5.640s passed
testUserExceptionOnAlleleDepthFieldSizeOneForMafOutput 0.867s passed
testVCFColumnsArentShuffled 0.106s passed
testVCFToMAFPreservesFields 0.114s passed
testVCFToVCFPreservesFields 0.115s passed
testVcfDatasourceAccountsForAltAlleles 0.104s passed
testVcfMafConcordance[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf, /tmp/funcotatorTmpFolder6727863116901585292/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 15) 0.229s passed
testVcfMafConcordance[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder6727863116901585292/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57) 0.272s passed
testVcfMafConcordance[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf, /tmp/funcotatorTmpFolder460415242273313878/GRCh37.p13.chr19.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, false, 2057) 33.732s passed
testVcfMafConcordance[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf, /tmp/funcotatorTmpFolder16217001170830957345/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) 0.436s passed
testVcfMafConcordance[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder6727863116901585292/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) 0.287s passed
testVcfToMafHonorsExcludedFields 0.110s passed
testXsvLocatableAnnotationsHaveCorrectColsForOnlyOnePositionSpecified 0.136s passed
testXsvLocatableAnnotationsHaveOnlyOneEntryForMultiHitLocations 0.132s passed

Standard error

15:55:43.557 INFO  Funcotator - ------------------------------------------------------------
15:55:43.557 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:55:43.557 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:43.557 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:55:43.557 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:55:43.557 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:55:43 PM GMT
15:55:43.557 INFO  Funcotator - ------------------------------------------------------------
15:55:43.557 INFO  Funcotator - ------------------------------------------------------------
15:55:43.557 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:55:43.557 INFO  Funcotator - Picard Version: 3.4.0
15:55:43.557 INFO  Funcotator - Built for Spark Version: 3.5.0
15:55:43.557 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:43.557 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:43.557 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:43.557 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:43.557 INFO  Funcotator - Deflater: IntelDeflater
15:55:43.558 INFO  Funcotator - Inflater: IntelInflater
15:55:43.558 INFO  Funcotator - GCS max retries/reopens: 20
15:55:43.558 INFO  Funcotator - Requester pays: disabled
15:55:43.558 INFO  Funcotator - Initializing engine
15:55:43.559 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:55:43.560 INFO  Funcotator - Done initializing engine
15:55:43.560 INFO  Funcotator - Skipping sequence dictionary validation.
15:55:43.560 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:55:43.560 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder9242384298607500784/TranscriptIdFile.txt
15:55:43.560 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:55:43.560 INFO  FuncotatorEngine - Transcript parsing complete.
15:55:43.561 INFO  Funcotator - Initializing data sources...
15:55:43.561 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:55:43.561 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:55:43.561 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
15:55:43.562 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
15:55:43.562 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
15:55:43.562 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
15:55:43.562 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
15:55:43.563 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
15:55:43.563 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:43.563 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:43.563 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
15:55:43.564 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
15:55:43.564 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
15:55:43.564 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
15:55:43.564 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:43.565 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
15:55:43.565 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
15:55:43.565 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:55:43.565 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
15:55:43.565 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
15:55:43.584 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
15:55:43.585 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
15:55:43.631 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
15:55:43.631 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
15:55:44.212 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:44.212 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:55:44.214 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:44.216 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:44.219 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:44.221 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:55:44.221 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:44.222 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:55:44.250 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:44.250 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:55:44	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:55:44.251 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
15:55:44.291 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
15:55:44.291 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
15:55:44.291 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
15:55:44.300 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:44.374 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
15:55:44.374 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:55:44.375 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:44.375 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
15:55:44.473 INFO  Funcotator - Initializing Funcotator Engine...
15:55:44.473 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
15:55:44.474 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:55:44.474 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:55:44.474 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:55:44.474 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:55:44.474 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:55:44.474 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:55:44.474 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:55:44.474 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:55:44.474 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:55:44.474 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:55:44.474 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:55:44.474 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:55:44.474 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:55:44.475 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:55:44.476 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:55:44.477 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:55:44.477 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:55:44.477 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.39582174036999712473.vcf
15:55:44.478 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
15:55:44.480 INFO  ProgressMeter - Starting traversal
15:55:44.480 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:55:44.550 INFO  ProgressMeter -             unmapped              0.0                     3           2571.4
15:55:44.550 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:55:44.551 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:55:44.554 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:55:44 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2355101696
15:55:44.646 INFO  Funcotator - ------------------------------------------------------------
15:55:44.646 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:55:44.646 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:44.646 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:55:44.646 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:55:44.646 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:55:44 PM GMT
15:55:44.646 INFO  Funcotator - ------------------------------------------------------------
15:55:44.646 INFO  Funcotator - ------------------------------------------------------------
15:55:44.646 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:55:44.646 INFO  Funcotator - Picard Version: 3.4.0
15:55:44.646 INFO  Funcotator - Built for Spark Version: 3.5.0
15:55:44.646 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:44.646 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:44.646 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:44.646 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:44.646 INFO  Funcotator - Deflater: IntelDeflater
15:55:44.646 INFO  Funcotator - Inflater: IntelInflater
15:55:44.646 INFO  Funcotator - GCS max retries/reopens: 20
15:55:44.646 INFO  Funcotator - Requester pays: disabled
15:55:44.646 INFO  Funcotator - Initializing engine
15:55:44.648 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:55:44.648 INFO  Funcotator - Done initializing engine
15:55:44.648 INFO  Funcotator - Skipping sequence dictionary validation.
15:55:44.648 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:55:44.648 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder18217699015919971295/TranscriptIdFile.txt
15:55:44.648 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:55:44.648 INFO  FuncotatorEngine - Transcript parsing complete.
15:55:44.648 INFO  Funcotator - Initializing data sources...
15:55:44.649 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:55:44.649 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:55:44.649 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
15:55:44.649 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
15:55:44.650 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
15:55:44.650 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:55:44.650 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:55:44.650 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
15:55:44.651 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:44.651 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:44.651 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
15:55:44.651 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
15:55:44.652 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:55:44.652 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:55:44.652 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:44.652 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
15:55:44.652 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
15:55:44.652 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:55:44.653 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:55:44.653 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:55:44.674 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
15:55:44.674 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
15:55:44.720 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
15:55:44.721 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
15:55:45.305 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:45.305 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:55:45.306 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:45.308 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
15:55:45.311 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:45.313 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:55:45.313 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
15:55:45.314 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:55:45.342 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:45.342 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:55:45	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:55:45.342 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
15:55:45.381 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
15:55:45.382 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
15:55:45.382 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
15:55:45.390 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:45.390 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
15:55:45.390 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:55:45.391 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:45.392 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
15:55:45.544 INFO  Funcotator - Initializing Funcotator Engine...
15:55:45.544 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:55:45.544 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:55:45.544 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.49322488089417424206.vcf
15:55:45.546 INFO  ProgressMeter - Starting traversal
15:55:45.546 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:55:45.708 INFO  ProgressMeter -             unmapped              0.0                     4           1481.5
15:55:45.708 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:55:45.708 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:55:45.709 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:55:45 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2355101696
15:55:45.817 INFO  Funcotator - ------------------------------------------------------------
15:55:45.817 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:55:45.817 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:45.817 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:55:45.817 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:55:45.817 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:55:45 PM GMT
15:55:45.817 INFO  Funcotator - ------------------------------------------------------------
15:55:45.817 INFO  Funcotator - ------------------------------------------------------------
15:55:45.817 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:55:45.817 INFO  Funcotator - Picard Version: 3.4.0
15:55:45.817 INFO  Funcotator - Built for Spark Version: 3.5.0
15:55:45.817 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:45.817 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:45.817 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:45.817 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:45.817 INFO  Funcotator - Deflater: IntelDeflater
15:55:45.817 INFO  Funcotator - Inflater: IntelInflater
15:55:45.817 INFO  Funcotator - GCS max retries/reopens: 20
15:55:45.817 INFO  Funcotator - Requester pays: disabled
15:55:45.817 INFO  Funcotator - Initializing engine
15:55:45.818 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:55:45.819 INFO  Funcotator - Done initializing engine
15:55:45.819 INFO  Funcotator - Skipping sequence dictionary validation.
15:55:45.819 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:55:45.819 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder2052811232302363916/TranscriptIdFile.txt
15:55:45.819 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:55:45.819 INFO  FuncotatorEngine - Transcript parsing complete.
15:55:45.819 INFO  Funcotator - Initializing data sources...
15:55:45.819 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:55:45.819 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:55:45.820 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:55:45.820 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:55:45.820 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:55:45.820 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
15:55:45.821 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
15:55:45.821 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
15:55:45.821 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:45.821 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
15:55:45.822 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
15:55:45.822 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
15:55:45.822 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
15:55:45.822 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:55:45.822 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:45.823 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
15:55:45.823 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
15:55:45.823 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:55:45.823 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
15:55:45.823 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
15:55:45.842 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
15:55:45.843 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
15:55:45.888 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:55:45.889 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
15:55:46.497 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:46.497 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:55:46.498 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:46.500 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:46.503 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:46.505 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:55:46.505 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:46.506 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:55:46.533 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
15:55:46.533 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
WARNING	2025-05-27 15:55:46	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:55:46.534 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
15:55:46.631 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
15:55:46.632 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
15:55:46.632 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
15:55:46.640 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:46.640 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
15:55:46.640 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:55:46.641 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:46.641 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
15:55:46.727 INFO  Funcotator - Initializing Funcotator Engine...
15:55:46.727 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
15:55:46.728 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:55:46.728 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:55:46.728 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:55:46.728 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:55:46.729 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:55:46.730 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:55:46.730 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:55:46.730 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.31356101235613914209.vcf
15:55:46.730 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
15:55:46.731 INFO  ProgressMeter - Starting traversal
15:55:46.731 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:55:46.754 INFO  ProgressMeter -             unmapped              0.0                     3           7826.1
15:55:46.754 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:55:46.754 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:55:46.756 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:55:46 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2355101696
15:55:46.848 INFO  Funcotator - ------------------------------------------------------------
15:55:46.848 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:55:46.848 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:46.848 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:55:46.848 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:55:46.848 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:55:46 PM GMT
15:55:46.848 INFO  Funcotator - ------------------------------------------------------------
15:55:46.848 INFO  Funcotator - ------------------------------------------------------------
15:55:46.848 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:55:46.848 INFO  Funcotator - Picard Version: 3.4.0
15:55:46.848 INFO  Funcotator - Built for Spark Version: 3.5.0
15:55:46.848 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:46.848 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:46.848 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:46.848 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:46.848 INFO  Funcotator - Deflater: IntelDeflater
15:55:46.848 INFO  Funcotator - Inflater: IntelInflater
15:55:46.848 INFO  Funcotator - GCS max retries/reopens: 20
15:55:46.848 INFO  Funcotator - Requester pays: disabled
15:55:46.848 INFO  Funcotator - Initializing engine
15:55:46.849 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:55:46.850 INFO  Funcotator - Done initializing engine
15:55:46.850 INFO  Funcotator - Skipping sequence dictionary validation.
15:55:46.850 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:55:46.850 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder4021339080583458014/TranscriptIdFile.txt
15:55:46.850 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:55:46.850 INFO  FuncotatorEngine - Transcript parsing complete.
15:55:46.850 INFO  Funcotator - Initializing data sources...
15:55:46.850 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:55:46.850 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:55:46.851 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
15:55:46.851 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
15:55:46.851 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
15:55:46.852 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
15:55:46.852 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
15:55:46.852 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
15:55:46.852 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:46.852 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:46.853 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
15:55:46.853 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
15:55:46.853 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
15:55:46.853 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
15:55:46.854 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:46.854 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
15:55:46.854 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
15:55:46.854 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:55:46.854 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
15:55:46.854 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
15:55:46.880 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
15:55:46.881 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
15:55:46.924 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
15:55:46.925 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
15:55:47.619 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:47.619 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:55:47.620 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:47.623 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
15:55:47.625 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:47.628 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:55:47.628 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:47.629 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:55:47.656 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:47.656 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:55:47	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:55:47.656 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
15:55:47.696 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
15:55:47.696 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
15:55:47.697 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
15:55:47.704 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:47.705 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:47.705 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:55:47.706 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:47.706 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:55:47.797 INFO  Funcotator - Initializing Funcotator Engine...
15:55:47.797 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:55:47.797 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:55:47.797 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.43335310201730161175.vcf
15:55:47.799 INFO  ProgressMeter - Starting traversal
15:55:47.799 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:55:47.904 INFO  ProgressMeter -             unmapped              0.0                     4           2285.7
15:55:47.904 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:55:47.904 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:55:47.905 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:55:47 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2485125120
15:55:48.047 INFO  Funcotator - ------------------------------------------------------------
15:55:48.047 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:55:48.047 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:48.047 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:55:48.047 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:55:48.047 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:55:48 PM GMT
15:55:48.047 INFO  Funcotator - ------------------------------------------------------------
15:55:48.047 INFO  Funcotator - ------------------------------------------------------------
15:55:48.047 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:55:48.047 INFO  Funcotator - Picard Version: 3.4.0
15:55:48.047 INFO  Funcotator - Built for Spark Version: 3.5.0
15:55:48.047 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:48.047 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:48.047 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:48.047 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:48.047 INFO  Funcotator - Deflater: IntelDeflater
15:55:48.047 INFO  Funcotator - Inflater: IntelInflater
15:55:48.047 INFO  Funcotator - GCS max retries/reopens: 20
15:55:48.047 INFO  Funcotator - Requester pays: disabled
15:55:48.047 INFO  Funcotator - Initializing engine
15:55:48.048 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:55:48.049 INFO  Funcotator - Done initializing engine
15:55:48.049 INFO  Funcotator - Skipping sequence dictionary validation.
15:55:48.049 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:55:48.049 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder1717866934043722516/TranscriptIdFile.txt
15:55:48.049 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:55:48.049 INFO  FuncotatorEngine - Transcript parsing complete.
15:55:48.049 INFO  Funcotator - Initializing data sources...
15:55:48.049 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:55:48.049 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:55:48.049 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
15:55:48.050 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
15:55:48.050 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
15:55:48.050 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
15:55:48.050 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
15:55:48.051 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
15:55:48.051 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:48.051 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:48.051 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
15:55:48.051 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
15:55:48.052 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
15:55:48.052 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
15:55:48.052 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:48.052 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
15:55:48.052 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
15:55:48.052 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:55:48.052 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:55:48.053 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
15:55:48.071 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
15:55:48.072 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
15:55:48.117 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
15:55:48.117 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
15:55:48.825 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:48.825 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:55:48.826 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:48.828 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:48.831 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:48.833 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:55:48.833 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:48.834 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:55:48.862 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:48.862 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:55:48	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:55:48.863 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
15:55:48.901 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:55:48.901 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:55:48.901 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
15:55:48.909 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:48.909 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
15:55:48.909 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:55:48.910 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:48.911 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
15:55:48.995 INFO  Funcotator - Initializing Funcotator Engine...
15:55:48.995 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
15:55:48.995 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:55:48.995 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:55:48.995 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:55:48.995 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:55:48.996 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:55:48.996 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:55:48.996 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.32777498463589713951.maf
15:55:48.998 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
15:55:49.000 INFO  ProgressMeter - Starting traversal
15:55:49.000 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:55:49.024 INFO  ProgressMeter -             unmapped              0.0                     3           7500.0
15:55:49.024 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:55:49.024 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:55:49.024 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:55:49 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2652897280
15:55:49.157 INFO  Funcotator - ------------------------------------------------------------
15:55:49.157 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:55:49.157 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:49.157 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:55:49.157 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:55:49.157 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:55:49 PM GMT
15:55:49.157 INFO  Funcotator - ------------------------------------------------------------
15:55:49.157 INFO  Funcotator - ------------------------------------------------------------
15:55:49.157 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:55:49.157 INFO  Funcotator - Picard Version: 3.4.0
15:55:49.157 INFO  Funcotator - Built for Spark Version: 3.5.0
15:55:49.157 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:49.157 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:49.157 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:49.157 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:49.157 INFO  Funcotator - Deflater: IntelDeflater
15:55:49.157 INFO  Funcotator - Inflater: IntelInflater
15:55:49.157 INFO  Funcotator - GCS max retries/reopens: 20
15:55:49.157 INFO  Funcotator - Requester pays: disabled
15:55:49.157 INFO  Funcotator - Initializing engine
15:55:49.158 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:55:49.159 INFO  Funcotator - Done initializing engine
15:55:49.159 INFO  Funcotator - Skipping sequence dictionary validation.
15:55:49.159 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:55:49.159 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder15663277906912057468/TranscriptIdFile.txt
15:55:49.159 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:55:49.159 INFO  FuncotatorEngine - Transcript parsing complete.
15:55:49.159 INFO  Funcotator - Initializing data sources...
15:55:49.159 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:55:49.159 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:55:49.159 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
15:55:49.160 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
15:55:49.160 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
15:55:49.160 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
15:55:49.160 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
15:55:49.160 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
15:55:49.161 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:49.161 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:49.161 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
15:55:49.161 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
15:55:49.161 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
15:55:49.162 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
15:55:49.162 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:49.162 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
15:55:49.162 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
15:55:49.162 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:55:49.162 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
15:55:49.162 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
15:55:49.182 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
15:55:49.182 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
15:55:49.228 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
15:55:49.229 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
15:55:49.836 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:49.836 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:55:49.837 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:49.839 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:49.842 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:49.844 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:55:49.844 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:49.845 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:55:49.872 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:49.873 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
WARNING	2025-05-27 15:55:49	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:55:49.873 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
15:55:49.943 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
15:55:49.943 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
15:55:49.944 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:55:49.966 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:49.966 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
15:55:49.966 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:55:49.967 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:49.968 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
15:55:50.070 INFO  Funcotator - Initializing Funcotator Engine...
15:55:50.070 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:55:50.070 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:55:50.070 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.42630347735718691500.maf
15:55:50.070 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
15:55:50.072 INFO  ProgressMeter - Starting traversal
15:55:50.072 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:55:50.174 INFO  ProgressMeter -             unmapped              0.0                     4           2376.2
15:55:50.174 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:55:50.174 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:55:50.174 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:55:50 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2730491904
15:55:50.310 INFO  Funcotator - ------------------------------------------------------------
15:55:50.310 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:55:50.310 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:50.310 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:55:50.310 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:55:50.310 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:55:50 PM GMT
15:55:50.310 INFO  Funcotator - ------------------------------------------------------------
15:55:50.310 INFO  Funcotator - ------------------------------------------------------------
15:55:50.310 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:55:50.310 INFO  Funcotator - Picard Version: 3.4.0
15:55:50.310 INFO  Funcotator - Built for Spark Version: 3.5.0
15:55:50.310 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:50.310 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:50.310 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:50.310 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:50.311 INFO  Funcotator - Deflater: IntelDeflater
15:55:50.311 INFO  Funcotator - Inflater: IntelInflater
15:55:50.311 INFO  Funcotator - GCS max retries/reopens: 20
15:55:50.311 INFO  Funcotator - Requester pays: disabled
15:55:50.311 INFO  Funcotator - Initializing engine
15:55:50.312 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:55:50.313 INFO  Funcotator - Done initializing engine
15:55:50.313 INFO  Funcotator - Skipping sequence dictionary validation.
15:55:50.313 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:55:50.313 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder13256456091387167769/TranscriptIdFile.txt
15:55:50.313 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:55:50.313 INFO  FuncotatorEngine - Transcript parsing complete.
15:55:50.313 INFO  Funcotator - Initializing data sources...
15:55:50.313 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:55:50.313 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:55:50.313 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
15:55:50.314 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
15:55:50.314 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:55:50.314 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
15:55:50.314 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:55:50.314 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
15:55:50.315 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:50.315 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:50.315 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
15:55:50.315 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
15:55:50.315 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
15:55:50.316 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
15:55:50.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:50.316 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
15:55:50.316 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
15:55:50.316 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:55:50.316 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
15:55:50.316 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:55:50.349 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
15:55:50.350 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
15:55:50.398 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
15:55:50.399 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
15:55:51.080 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:51.080 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:55:51.081 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:51.084 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:51.086 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:51.089 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:55:51.089 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
15:55:51.089 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:55:51.117 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:51.117 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:55:51	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:55:51.118 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
15:55:51.157 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
15:55:51.157 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
15:55:51.157 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
15:55:51.165 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:51.166 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
15:55:51.166 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:55:51.167 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:51.167 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
15:55:51.259 INFO  Funcotator - Initializing Funcotator Engine...
15:55:51.259 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
15:55:51.259 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:55:51.260 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:55:51.260 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:55:51.260 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:55:51.260 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:55:51.260 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.36798308034789601002.maf
15:55:51.261 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
15:55:51.262 INFO  ProgressMeter - Starting traversal
15:55:51.262 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:55:51.282 INFO  ProgressMeter -             unmapped              0.0                     3           9000.0
15:55:51.282 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:55:51.282 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:55:51.283 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:55:51 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2833252352
15:55:51.375 INFO  Funcotator - ------------------------------------------------------------
15:55:51.375 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:55:51.375 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:51.375 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:55:51.375 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:55:51.375 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:55:51 PM GMT
15:55:51.375 INFO  Funcotator - ------------------------------------------------------------
15:55:51.375 INFO  Funcotator - ------------------------------------------------------------
15:55:51.375 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:55:51.375 INFO  Funcotator - Picard Version: 3.4.0
15:55:51.375 INFO  Funcotator - Built for Spark Version: 3.5.0
15:55:51.376 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:51.376 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:51.376 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:51.376 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:51.376 INFO  Funcotator - Deflater: IntelDeflater
15:55:51.376 INFO  Funcotator - Inflater: IntelInflater
15:55:51.376 INFO  Funcotator - GCS max retries/reopens: 20
15:55:51.376 INFO  Funcotator - Requester pays: disabled
15:55:51.376 INFO  Funcotator - Initializing engine
15:55:51.377 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:55:51.377 INFO  Funcotator - Done initializing engine
15:55:51.377 INFO  Funcotator - Skipping sequence dictionary validation.
15:55:51.377 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:55:51.377 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder14857186087813848212/TranscriptIdFile.txt
15:55:51.377 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:55:51.377 INFO  FuncotatorEngine - Transcript parsing complete.
15:55:51.377 INFO  Funcotator - Initializing data sources...
15:55:51.377 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:55:51.377 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:55:51.378 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
15:55:51.378 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
15:55:51.378 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
15:55:51.378 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
15:55:51.379 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
15:55:51.379 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
15:55:51.379 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:51.379 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:51.379 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
15:55:51.380 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:55:51.380 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:55:51.380 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
15:55:51.380 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:51.380 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
15:55:51.380 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
15:55:51.380 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:55:51.381 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
15:55:51.381 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
15:55:51.400 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
15:55:51.400 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
15:55:51.445 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
15:55:51.446 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
15:55:52.101 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:52.101 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:55:52.102 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:52.104 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:52.107 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:52.109 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:55:52.109 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:52.110 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:55:52.137 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:52.137 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:55:52	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:55:52.138 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
15:55:52.177 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
15:55:52.177 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
15:55:52.178 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
15:55:52.185 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:52.186 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
15:55:52.186 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:55:52.187 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:52.187 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
15:55:52.274 INFO  Funcotator - Initializing Funcotator Engine...
15:55:52.274 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:55:52.274 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:55:52.274 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.46375063469561555412.maf
15:55:52.274 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
15:55:52.276 INFO  ProgressMeter - Starting traversal
15:55:52.276 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:55:52.386 INFO  ProgressMeter -             unmapped              0.0                     4           2181.8
15:55:52.386 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:55:52.387 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:55:52.387 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:55:52 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2833252352
15:55:52.490 INFO  Funcotator - ------------------------------------------------------------
15:55:52.490 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:55:52.490 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:52.491 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:55:52.491 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:55:52.491 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:55:52 PM GMT
15:55:52.491 INFO  Funcotator - ------------------------------------------------------------
15:55:52.491 INFO  Funcotator - ------------------------------------------------------------
15:55:52.491 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:55:52.491 INFO  Funcotator - Picard Version: 3.4.0
15:55:52.491 INFO  Funcotator - Built for Spark Version: 3.5.0
15:55:52.491 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:52.491 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:52.491 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:52.491 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:52.491 INFO  Funcotator - Deflater: IntelDeflater
15:55:52.491 INFO  Funcotator - Inflater: IntelInflater
15:55:52.491 INFO  Funcotator - GCS max retries/reopens: 20
15:55:52.491 INFO  Funcotator - Requester pays: disabled
15:55:52.491 INFO  Funcotator - Initializing engine
15:55:52.493 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
15:55:52.494 INFO  Funcotator - Done initializing engine
15:55:52.494 INFO  Funcotator - Validating sequence dictionaries...
15:55:52.495 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:55:52.495 INFO  Funcotator - Initializing data sources...
15:55:52.495 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:55:52.495 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:55:52.495 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
15:55:52.495 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
15:55:52.496 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
15:55:52.496 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
15:55:52.496 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
15:55:52.496 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
15:55:52.496 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:52.497 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
15:55:52.497 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
15:55:52.497 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
15:55:52.497 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
15:55:52.497 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
15:55:52.498 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:52.498 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
15:55:52.498 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
15:55:52.498 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:55:52.498 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
15:55:52.498 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
15:55:52.517 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
15:55:52.518 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
15:55:52.563 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
15:55:52.563 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
15:55:53.179 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:53.179 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:55:53.180 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:53.182 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
15:55:53.185 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:53.187 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:55:53.188 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:53.188 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:55:53.216 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
15:55:53.216 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	2025-05-27 15:55:53	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:55:53.216 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
15:55:53.321 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
15:55:53.321 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
15:55:53.322 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
15:55:53.329 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:53.330 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
15:55:53.330 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:55:53.331 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:53.331 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
15:55:53.416 INFO  Funcotator - Initializing Funcotator Engine...
15:55:53.416 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:55:53.416 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
15:55:53.416 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator15879882103176014642.vcf
15:55:53.418 INFO  ProgressMeter - Starting traversal
15:55:53.418 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:55:55.592 INFO  ProgressMeter -             unmapped              0.0                   198           5464.6
15:55:55.592 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:55:55.592 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:55:55.601 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:55:55 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3135242240
15:55:55.602 WARN  gatk -   VCF Elapsed Time: 3.21300311s
15:55:55.603 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet1.vcf.funcotator15879882103176014642.vcf
15:55:55.605 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
15:55:55.714 INFO  Funcotator - ------------------------------------------------------------
15:55:55.714 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:55:55.714 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:55.714 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:55:55.714 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:55:55.714 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:55:55 PM GMT
15:55:55.715 INFO  Funcotator - ------------------------------------------------------------
15:55:55.715 INFO  Funcotator - ------------------------------------------------------------
15:55:55.715 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:55:55.715 INFO  Funcotator - Picard Version: 3.4.0
15:55:55.715 INFO  Funcotator - Built for Spark Version: 3.5.0
15:55:55.715 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:55.715 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:55.715 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:55.715 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:55.715 INFO  Funcotator - Deflater: IntelDeflater
15:55:55.715 INFO  Funcotator - Inflater: IntelInflater
15:55:55.715 INFO  Funcotator - GCS max retries/reopens: 20
15:55:55.715 INFO  Funcotator - Requester pays: disabled
15:55:55.715 INFO  Funcotator - Initializing engine
15:55:55.717 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
15:55:55.718 INFO  Funcotator - Done initializing engine
15:55:55.718 INFO  Funcotator - Validating sequence dictionaries...
15:55:55.718 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:55:55.718 INFO  Funcotator - Initializing data sources...
15:55:55.718 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:55:55.718 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:55:55.719 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
15:55:55.719 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
15:55:55.719 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
15:55:55.719 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
15:55:55.720 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
15:55:55.720 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
15:55:55.720 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:55.720 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:55.720 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
15:55:55.721 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
15:55:55.721 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
15:55:55.721 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
15:55:55.721 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:55.721 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:55.721 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
15:55:55.721 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:55:55.721 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
15:55:55.722 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
15:55:55.741 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
15:55:55.742 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
15:55:55.787 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
15:55:55.787 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
15:55:56.371 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:56.372 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:55:56.373 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:56.375 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
15:55:56.377 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:56.379 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:55:56.380 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
15:55:56.380 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:55:56.408 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
15:55:56.408 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
WARNING	2025-05-27 15:55:56	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:55:56.408 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
15:55:56.447 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
15:55:56.448 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
15:55:56.448 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
15:55:56.456 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:56.456 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
15:55:56.456 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:55:56.457 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:56.457 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
15:55:56.542 INFO  Funcotator - Initializing Funcotator Engine...
15:55:56.543 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:55:56.543 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.
15:55:56.543 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator16627835296954662724.maf
15:55:56.543 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
15:55:56.545 INFO  ProgressMeter - Starting traversal
15:55:56.545 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:55:58.537 INFO  ProgressMeter -             unmapped              0.0                   198           5963.9
15:55:58.537 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:55:58.537 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:55:58.538 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:55:58 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3135242240
15:55:58.538 WARN  gatk -   MAF Elapsed Time: 2.920675107s
15:55:58.643 INFO  Funcotator - ------------------------------------------------------------
15:55:58.644 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:55:58.644 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:58.644 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:55:58.644 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:55:58.644 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:55:58 PM GMT
15:55:58.644 INFO  Funcotator - ------------------------------------------------------------
15:55:58.644 INFO  Funcotator - ------------------------------------------------------------
15:55:58.644 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:55:58.644 INFO  Funcotator - Picard Version: 3.4.0
15:55:58.644 INFO  Funcotator - Built for Spark Version: 3.5.0
15:55:58.644 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:58.644 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:58.644 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:58.644 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:58.644 INFO  Funcotator - Deflater: IntelDeflater
15:55:58.644 INFO  Funcotator - Inflater: IntelInflater
15:55:58.644 INFO  Funcotator - GCS max retries/reopens: 20
15:55:58.644 INFO  Funcotator - Requester pays: disabled
15:55:58.644 INFO  Funcotator - Initializing engine
15:55:58.646 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
15:55:58.647 INFO  Funcotator - Done initializing engine
15:55:58.647 INFO  Funcotator - Validating sequence dictionaries...
15:55:58.648 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:55:58.648 INFO  Funcotator - Initializing data sources...
15:55:58.648 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:55:58.648 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:55:58.648 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
15:55:58.648 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
15:55:58.648 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
15:55:58.649 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
15:55:58.649 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
15:55:58.649 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
15:55:58.649 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:58.649 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:58.650 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
15:55:58.650 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
15:55:58.650 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
15:55:58.650 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
15:55:58.650 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:58.650 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
15:55:58.651 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
15:55:58.651 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:55:58.651 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:55:58.651 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:55:58.670 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
15:55:58.671 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
15:55:58.716 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
15:55:58.716 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
15:55:59.293 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:59.293 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:55:59.295 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:59.297 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:59.299 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:55:59.301 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:55:59.302 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:59.302 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:55:59.330 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:55:59.330 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:55:59	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:55:59.331 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
15:55:59.370 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
15:55:59.370 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
15:55:59.370 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
15:55:59.378 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:55:59.379 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
15:55:59.379 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:55:59.379 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:55:59.380 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
15:55:59.465 INFO  Funcotator - Initializing Funcotator Engine...
15:55:59.465 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:55:59.465 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.
15:55:59.465 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator6558123949956959204.vcf
15:55:59.467 INFO  ProgressMeter - Starting traversal
15:55:59.467 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:00.481 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:56:00.481 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:56:01.227 INFO  ProgressMeter -             unmapped              0.0                   168           5727.3
15:56:01.227 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
15:56:01.227 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
15:56:01.232 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:01 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=3135242240
15:56:01.233 WARN  gatk -   VCF Elapsed Time: 2.692493296s
15:56:01.233 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet2.vcf.funcotator6558123949956959204.vcf
15:56:01.235 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf
15:56:01.330 INFO  Funcotator - ------------------------------------------------------------
15:56:01.330 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:01.330 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:01.330 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:01.331 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:01.331 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:01 PM GMT
15:56:01.331 INFO  Funcotator - ------------------------------------------------------------
15:56:01.331 INFO  Funcotator - ------------------------------------------------------------
15:56:01.331 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:01.331 INFO  Funcotator - Picard Version: 3.4.0
15:56:01.331 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:01.331 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:01.331 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:01.331 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:01.331 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:01.331 INFO  Funcotator - Deflater: IntelDeflater
15:56:01.331 INFO  Funcotator - Inflater: IntelInflater
15:56:01.331 INFO  Funcotator - GCS max retries/reopens: 20
15:56:01.331 INFO  Funcotator - Requester pays: disabled
15:56:01.331 INFO  Funcotator - Initializing engine
15:56:01.333 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
15:56:01.334 INFO  Funcotator - Done initializing engine
15:56:01.334 INFO  Funcotator - Validating sequence dictionaries...
15:56:01.335 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:01.335 INFO  Funcotator - Initializing data sources...
15:56:01.335 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:01.335 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:01.335 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:56:01.335 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
15:56:01.335 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
15:56:01.336 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
15:56:01.336 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
15:56:01.336 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
15:56:01.336 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:01.336 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:01.336 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
15:56:01.336 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
15:56:01.337 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
15:56:01.337 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
15:56:01.337 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:01.337 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
15:56:01.337 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
15:56:01.337 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:01.337 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
15:56:01.337 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
15:56:01.356 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
15:56:01.357 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
15:56:01.402 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:56:01.402 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:56:01.971 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:01.971 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:01.972 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:01.975 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:01.978 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:01.980 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:01.980 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:01.981 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:02.049 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:02.049 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:02	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:02.049 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
15:56:02.089 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
15:56:02.090 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
15:56:02.090 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
15:56:02.098 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:02.098 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
15:56:02.098 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:02.099 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:02.099 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
15:56:02.184 INFO  Funcotator - Initializing Funcotator Engine...
15:56:02.185 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:56:02.185 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.
15:56:02.185 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator17996210816788214277.maf
15:56:02.185 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
15:56:02.186 INFO  ProgressMeter - Starting traversal
15:56:02.186 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:03.161 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:56:03.161 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:56:03.898 INFO  ProgressMeter -             unmapped              0.0                   168           5887.9
15:56:03.898 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
15:56:03.899 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
15:56:03.899 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:03 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=3158310912
15:56:03.899 WARN  gatk -   MAF Elapsed Time: 2.659369749s
15:56:03.997 INFO  Funcotator - ------------------------------------------------------------
15:56:03.997 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:03.997 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:03.997 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:03.997 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:03.997 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:03 PM GMT
15:56:03.997 INFO  Funcotator - ------------------------------------------------------------
15:56:03.997 INFO  Funcotator - ------------------------------------------------------------
15:56:03.997 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:03.997 INFO  Funcotator - Picard Version: 3.4.0
15:56:03.997 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:03.997 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:03.997 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:03.997 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:03.997 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:03.997 INFO  Funcotator - Deflater: IntelDeflater
15:56:03.997 INFO  Funcotator - Inflater: IntelInflater
15:56:03.997 INFO  Funcotator - GCS max retries/reopens: 20
15:56:03.997 INFO  Funcotator - Requester pays: disabled
15:56:03.997 INFO  Funcotator - Initializing engine
15:56:04.000 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
15:56:04.001 INFO  Funcotator - Done initializing engine
15:56:04.001 INFO  Funcotator - Validating sequence dictionaries...
15:56:04.001 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:04.001 INFO  Funcotator - Initializing data sources...
15:56:04.001 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:04.001 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:04.001 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:56:04.001 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:56:04.002 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
15:56:04.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:56:04.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:56:04.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:56:04.002 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
15:56:04.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:04.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:56:04.016 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
15:56:04.016 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
15:56:04.016 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
15:56:04.017 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:04.017 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
15:56:04.017 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
15:56:04.017 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:04.017 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
15:56:04.017 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
15:56:04.036 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
15:56:04.037 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:56:04.082 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
15:56:04.082 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
15:56:04.685 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
15:56:04.685 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:04.686 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:04.688 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:04.691 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:04.693 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:04.693 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:04.694 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:04.721 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:04.721 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:04	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:04.721 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:56:04.760 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
15:56:04.761 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
15:56:04.761 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
15:56:04.769 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:04.769 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
15:56:04.769 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:04.770 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:04.770 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
15:56:04.854 INFO  Funcotator - Initializing Funcotator Engine...
15:56:04.855 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:56:04.855 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.
15:56:04.855 INFO  Funcotator - Creating a VCF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator8774836149885061079.vcf
15:56:04.856 INFO  ProgressMeter - Starting traversal
15:56:04.856 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:04.866 INFO  ProgressMeter -             unmapped              0.0                     1           6000.0
15:56:04.866 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:56:04.866 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:56:04.868 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:04 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3158310912
15:56:04.868 WARN  gatk -   VCF Elapsed Time: 0.966446926s
15:56:04.868 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/hashSetOrderingIssue.vcf.funcotator8774836149885061079.vcf
15:56:04.870 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf
15:56:04.969 INFO  Funcotator - ------------------------------------------------------------
15:56:04.969 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:04.969 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:04.969 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:04.969 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:04.969 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:04 PM GMT
15:56:04.969 INFO  Funcotator - ------------------------------------------------------------
15:56:04.969 INFO  Funcotator - ------------------------------------------------------------
15:56:04.969 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:04.969 INFO  Funcotator - Picard Version: 3.4.0
15:56:04.969 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:04.969 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:04.969 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:04.969 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:04.969 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:04.969 INFO  Funcotator - Deflater: IntelDeflater
15:56:04.969 INFO  Funcotator - Inflater: IntelInflater
15:56:04.969 INFO  Funcotator - GCS max retries/reopens: 20
15:56:04.969 INFO  Funcotator - Requester pays: disabled
15:56:04.969 INFO  Funcotator - Initializing engine
15:56:04.972 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
15:56:04.973 INFO  Funcotator - Done initializing engine
15:56:04.973 INFO  Funcotator - Validating sequence dictionaries...
15:56:04.973 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:04.973 INFO  Funcotator - Initializing data sources...
15:56:04.973 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:04.973 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:04.973 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
15:56:04.973 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
15:56:04.974 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
15:56:04.974 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
15:56:04.974 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
15:56:04.974 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
15:56:04.974 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:04.974 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:04.975 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
15:56:04.975 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:56:04.975 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:56:04.975 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
15:56:04.975 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:04.976 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
15:56:04.976 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
15:56:04.976 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:04.976 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
15:56:04.976 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
15:56:04.995 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
15:56:04.995 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
15:56:05.041 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
15:56:05.041 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
15:56:05.721 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:05.721 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:05.722 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:05.724 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:05.727 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:05.729 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:05.730 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:05.730 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:05.758 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:05.758 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:05	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:05.758 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
15:56:05.798 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:56:05.798 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
15:56:05.799 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:56:05.807 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:05.807 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
15:56:05.807 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:05.808 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:05.808 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
15:56:05.892 INFO  Funcotator - Initializing Funcotator Engine...
15:56:05.892 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:56:05.892 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.
15:56:05.893 INFO  Funcotator - Creating a MAF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator17344471534654061618.maf
15:56:05.893 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
15:56:05.894 INFO  ProgressMeter - Starting traversal
15:56:05.894 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:05.904 INFO  ProgressMeter -             unmapped              0.0                     1           6000.0
15:56:05.904 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:56:05.904 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:56:05.904 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3158310912
15:56:05.904 WARN  gatk -   MAF Elapsed Time: 1.033497894s
15:56:06.090 INFO  Funcotator - ------------------------------------------------------------
15:56:06.090 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:06.090 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:06.090 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:06.090 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:06.090 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:06 PM GMT
15:56:06.090 INFO  Funcotator - ------------------------------------------------------------
15:56:06.090 INFO  Funcotator - ------------------------------------------------------------
15:56:06.090 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:06.090 INFO  Funcotator - Picard Version: 3.4.0
15:56:06.090 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:06.090 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:06.091 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:06.091 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:06.091 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:06.091 INFO  Funcotator - Deflater: IntelDeflater
15:56:06.091 INFO  Funcotator - Inflater: IntelInflater
15:56:06.091 INFO  Funcotator - GCS max retries/reopens: 20
15:56:06.091 INFO  Funcotator - Requester pays: disabled
15:56:06.091 INFO  Funcotator - Initializing engine
15:56:06.136 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
15:56:06.162 INFO  Funcotator - Done initializing engine
15:56:06.162 INFO  Funcotator - Validating sequence dictionaries...
15:56:06.168 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:06.168 INFO  Funcotator - Initializing data sources...
15:56:06.168 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:06.168 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:06.169 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
15:56:06.169 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
15:56:06.169 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
15:56:06.170 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
15:56:06.170 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
15:56:06.170 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
15:56:06.170 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
15:56:06.170 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
15:56:06.171 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
15:56:06.171 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
15:56:06.171 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
15:56:06.171 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
15:56:06.171 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
15:56:06.171 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:06.171 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
15:56:06.172 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
15:56:06.191 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
15:56:06.191 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
15:56:06.237 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
15:56:06.238 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
15:56:06.755 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
15:56:06.755 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:06.756 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:56:06.758 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
15:56:06.760 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:56:06.761 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
15:56:06.827 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
15:56:06.828 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
15:56:06.828 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
15:56:06.835 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
15:56:06.835 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:06.836 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
15:56:06.836 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
15:56:06.837 INFO  Funcotator - Initializing Funcotator Engine...
15:56:06.841 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:06.842 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator7366996447968236648.vcf
15:56:06.855 INFO  ProgressMeter - Starting traversal
15:56:06.855 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:06.880 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.
15:56:06.882 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
15:56:06.885 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:56:06.888 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:56:06.888 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:56:06.888 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:56:06.888 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:56:06.888 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:56:06.889 INFO  ProgressMeter -             unmapped              0.0                     5           8823.5
15:56:06.889 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
15:56:06.889 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:56:06.901 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:06 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360
15:56:06.901 WARN  gatk -   VCF Elapsed Time: 0.996102023s
15:56:06.901 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSetHG38.vcf.funcotator7366996447968236648.vcf
15:56:06.911 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf
15:56:07.012 INFO  Funcotator - ------------------------------------------------------------
15:56:07.012 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:07.012 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:07.012 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:07.012 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:07.012 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:07 PM GMT
15:56:07.012 INFO  Funcotator - ------------------------------------------------------------
15:56:07.012 INFO  Funcotator - ------------------------------------------------------------
15:56:07.012 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:07.012 INFO  Funcotator - Picard Version: 3.4.0
15:56:07.012 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:07.012 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:07.012 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:07.012 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:07.012 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:07.012 INFO  Funcotator - Deflater: IntelDeflater
15:56:07.012 INFO  Funcotator - Inflater: IntelInflater
15:56:07.012 INFO  Funcotator - GCS max retries/reopens: 20
15:56:07.012 INFO  Funcotator - Requester pays: disabled
15:56:07.012 INFO  Funcotator - Initializing engine
15:56:07.043 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
15:56:07.065 INFO  Funcotator - Done initializing engine
15:56:07.065 INFO  Funcotator - Validating sequence dictionaries...
15:56:07.072 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:07.072 INFO  Funcotator - Initializing data sources...
15:56:07.072 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:07.072 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:07.073 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
15:56:07.073 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
15:56:07.073 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
15:56:07.073 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
15:56:07.073 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
15:56:07.073 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
15:56:07.074 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
15:56:07.074 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
15:56:07.074 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
15:56:07.074 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
15:56:07.074 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
15:56:07.075 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
15:56:07.075 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
15:56:07.075 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:07.075 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
15:56:07.075 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
15:56:07.094 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:56:07.095 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
15:56:07.140 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
15:56:07.140 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
15:56:07.668 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
15:56:07.668 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:07.669 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:56:07.670 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
15:56:07.672 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:56:07.673 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
15:56:07.738 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
15:56:07.738 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
15:56:07.739 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
15:56:07.746 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
15:56:07.746 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:07.747 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
15:56:07.747 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
15:56:07.748 INFO  Funcotator - Initializing Funcotator Engine...
15:56:07.752 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:07.752 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator7053552761213612155.maf
15:56:07.754 INFO  ProgressMeter - Starting traversal
15:56:07.754 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:07.777 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.
15:56:07.777 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
15:56:07.778 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:56:07.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:56:07.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:56:07.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:56:07.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:56:07.782 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:56:07.783 INFO  ProgressMeter -             unmapped              0.0                     5          10344.8
15:56:07.783 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
15:56:07.783 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:56:07.783 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:07 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360
15:56:07.784 WARN  gatk -   MAF Elapsed Time: 0.865281733s
15:56:07.880 INFO  Funcotator - ------------------------------------------------------------
15:56:07.880 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:07.880 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:07.880 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:07.880 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:07.880 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:07 PM GMT
15:56:07.880 INFO  Funcotator - ------------------------------------------------------------
15:56:07.880 INFO  Funcotator - ------------------------------------------------------------
15:56:07.880 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:07.880 INFO  Funcotator - Picard Version: 3.4.0
15:56:07.880 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:07.880 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:07.880 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:07.880 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:07.880 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:07.880 INFO  Funcotator - Deflater: IntelDeflater
15:56:07.880 INFO  Funcotator - Inflater: IntelInflater
15:56:07.880 INFO  Funcotator - GCS max retries/reopens: 20
15:56:07.880 INFO  Funcotator - Requester pays: disabled
15:56:07.880 INFO  Funcotator - Initializing engine
15:56:07.883 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
15:56:07.884 INFO  Funcotator - Done initializing engine
15:56:07.884 INFO  Funcotator - Validating sequence dictionaries...
15:56:07.884 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:07.884 INFO  Funcotator - Initializing data sources...
15:56:07.885 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:07.885 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:07.885 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
15:56:07.885 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
15:56:07.885 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
15:56:07.885 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
15:56:07.886 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
15:56:07.886 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
15:56:07.886 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:07.886 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:07.886 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
15:56:07.886 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
15:56:07.886 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
15:56:07.887 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
15:56:07.887 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:07.887 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
15:56:07.887 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
15:56:07.887 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:07.887 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
15:56:07.887 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
15:56:07.906 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
15:56:07.907 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
15:56:07.952 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
15:56:07.952 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:56:08.483 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:08.483 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:08.484 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:08.486 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:08.489 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:08.491 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:08.492 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:08.492 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:08.519 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:08.520 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:08	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:08.520 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:56:08.559 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
15:56:08.559 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
15:56:08.559 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
15:56:08.567 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:08.567 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
15:56:08.567 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:08.568 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:08.568 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
15:56:08.652 INFO  Funcotator - Initializing Funcotator Engine...
15:56:08.653 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:56:08.653 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.
15:56:08.653 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator2516269202683573680.vcf
15:56:08.657 INFO  ProgressMeter - Starting traversal
15:56:08.657 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:13.987 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
15:56:13.988 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
15:56:13.989 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          16958.0
15:56:13.989 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
15:56:13.989 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
15:56:14.011 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:14 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3261071360
15:56:14.012 WARN  gatk -   VCF Elapsed Time: 6.22617918s
15:56:14.012 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestHg19Large.vcf.funcotator2516269202683573680.vcf
15:56:14.020 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf
15:56:14.145 INFO  Funcotator - ------------------------------------------------------------
15:56:14.145 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:14.145 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:14.145 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:14.145 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:14.145 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:14 PM GMT
15:56:14.145 INFO  Funcotator - ------------------------------------------------------------
15:56:14.145 INFO  Funcotator - ------------------------------------------------------------
15:56:14.145 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:14.145 INFO  Funcotator - Picard Version: 3.4.0
15:56:14.146 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:14.146 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:14.146 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:14.146 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:14.146 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:14.146 INFO  Funcotator - Deflater: IntelDeflater
15:56:14.146 INFO  Funcotator - Inflater: IntelInflater
15:56:14.146 INFO  Funcotator - GCS max retries/reopens: 20
15:56:14.146 INFO  Funcotator - Requester pays: disabled
15:56:14.146 INFO  Funcotator - Initializing engine
15:56:14.148 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
15:56:14.149 INFO  Funcotator - Done initializing engine
15:56:14.149 INFO  Funcotator - Validating sequence dictionaries...
15:56:14.149 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:14.149 INFO  Funcotator - Initializing data sources...
15:56:14.149 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:14.149 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:14.150 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
15:56:14.150 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
15:56:14.150 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:56:14.151 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
15:56:14.151 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
15:56:14.151 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
15:56:14.151 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:14.151 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:14.152 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
15:56:14.152 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
15:56:14.152 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
15:56:14.152 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
15:56:14.152 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:14.152 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
15:56:14.153 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
15:56:14.153 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:14.153 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
15:56:14.153 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
15:56:14.172 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
15:56:14.172 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
15:56:14.217 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
15:56:14.218 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
15:56:14.800 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:14.800 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:14.801 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:14.803 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:14.805 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:14.807 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:14.808 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:14.808 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:14.836 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:14.836 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:14	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:14.836 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:56:14.875 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
15:56:14.875 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
15:56:14.875 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
15:56:14.883 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:14.884 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
15:56:14.884 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:14.884 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:14.885 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
15:56:14.970 INFO  Funcotator - Initializing Funcotator Engine...
15:56:14.970 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:56:14.970 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.
15:56:14.970 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator9154627896576120647.maf
15:56:14.971 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
15:56:14.971 INFO  ProgressMeter - Starting traversal
15:56:14.971 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:20.007 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
15:56:20.007 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
15:56:20.008 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          17951.2
15:56:20.008 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
15:56:20.008 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
15:56:20.008 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:20 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3261071360
15:56:20.009 WARN  gatk -   MAF Elapsed Time: 5.968699423s
15:56:20.123 INFO  Funcotator - ------------------------------------------------------------
15:56:20.123 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:20.123 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:20.123 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:20.123 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:20.123 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:20 PM GMT
15:56:20.123 INFO  Funcotator - ------------------------------------------------------------
15:56:20.123 INFO  Funcotator - ------------------------------------------------------------
15:56:20.123 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:20.123 INFO  Funcotator - Picard Version: 3.4.0
15:56:20.123 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:20.123 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:20.123 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:20.123 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:20.123 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:20.123 INFO  Funcotator - Deflater: IntelDeflater
15:56:20.123 INFO  Funcotator - Inflater: IntelInflater
15:56:20.123 INFO  Funcotator - GCS max retries/reopens: 20
15:56:20.123 INFO  Funcotator - Requester pays: disabled
15:56:20.123 INFO  Funcotator - Initializing engine
15:56:20.125 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
15:56:20.126 INFO  Funcotator - Done initializing engine
15:56:20.127 INFO  Funcotator - Validating sequence dictionaries...
15:56:20.127 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:20.127 INFO  Funcotator - Initializing data sources...
15:56:20.127 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:20.127 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:20.127 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
15:56:20.127 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
15:56:20.128 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:56:20.128 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
15:56:20.128 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
15:56:20.128 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
15:56:20.128 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:20.129 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:20.129 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
15:56:20.129 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
15:56:20.129 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
15:56:20.129 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
15:56:20.130 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:20.130 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
15:56:20.130 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
15:56:20.130 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:20.130 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
15:56:20.130 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
15:56:20.149 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
15:56:20.150 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:56:20.195 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
15:56:20.195 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
15:56:20.743 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:20.743 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:20.744 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:20.746 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:20.749 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:20.751 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:20.751 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:20.752 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:20.786 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:20.786 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:20.786 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
15:56:20.901 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:56:20.901 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:56:20.902 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
15:56:20.909 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:20.910 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
15:56:20.910 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:20.911 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:20.911 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
15:56:20.997 INFO  Funcotator - Initializing Funcotator Engine...
15:56:20.997 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:56:20.997 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.
15:56:20.997 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator8458700930295888524.vcf
15:56:20.999 INFO  ProgressMeter - Starting traversal
15:56:20.999 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:22.944 INFO  ProgressMeter -             unmapped              0.0                   198           6108.0
15:56:22.944 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:56:22.944 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:56:22.953 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:22 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3261071360
15:56:23.049 INFO  Funcotator - ------------------------------------------------------------
15:56:23.049 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:23.049 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:23.049 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:23.049 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:23.049 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:23 PM GMT
15:56:23.049 INFO  Funcotator - ------------------------------------------------------------
15:56:23.049 INFO  Funcotator - ------------------------------------------------------------
15:56:23.050 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:23.050 INFO  Funcotator - Picard Version: 3.4.0
15:56:23.050 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:23.050 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:23.050 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:23.050 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:23.050 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:23.050 INFO  Funcotator - Deflater: IntelDeflater
15:56:23.050 INFO  Funcotator - Inflater: IntelInflater
15:56:23.050 INFO  Funcotator - GCS max retries/reopens: 20
15:56:23.050 INFO  Funcotator - Requester pays: disabled
15:56:23.050 INFO  Funcotator - Initializing engine
15:56:23.052 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
15:56:23.054 INFO  Funcotator - Done initializing engine
15:56:23.054 INFO  Funcotator - Validating sequence dictionaries...
15:56:23.054 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:23.054 INFO  Funcotator - Initializing data sources...
15:56:23.054 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:23.054 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:23.054 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
15:56:23.055 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:56:23.055 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
15:56:23.055 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
15:56:23.055 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
15:56:23.055 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
15:56:23.055 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:23.056 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:23.056 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
15:56:23.056 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
15:56:23.056 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
15:56:23.056 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
15:56:23.056 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:23.057 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
15:56:23.057 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
15:56:23.057 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:23.057 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:56:23.057 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:56:23.077 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
15:56:23.077 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
15:56:23.124 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:56:23.124 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:56:23.665 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:23.665 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:23.666 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:23.668 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:23.671 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:23.673 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:23.673 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
15:56:23.674 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:23.702 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:23.702 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:23	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:23.702 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
15:56:23.742 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
15:56:23.743 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
15:56:23.743 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
15:56:23.751 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:23.751 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:23.751 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:23.752 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:23.753 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:56:23.836 INFO  Funcotator - Initializing Funcotator Engine...
15:56:23.836 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:56:23.836 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.
15:56:23.836 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator16669018800008702674.maf
15:56:23.837 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
15:56:23.837 INFO  ProgressMeter - Starting traversal
15:56:23.837 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:25.760 INFO  ProgressMeter -             unmapped              0.0                   198           6177.8
15:56:25.761 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:56:25.761 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:56:25.761 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:25 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3261071360
15:56:25.855 INFO  Funcotator - ------------------------------------------------------------
15:56:25.855 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:25.855 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:25.856 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:25.856 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:25.856 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:25 PM GMT
15:56:25.856 INFO  Funcotator - ------------------------------------------------------------
15:56:25.856 INFO  Funcotator - ------------------------------------------------------------
15:56:25.856 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:25.856 INFO  Funcotator - Picard Version: 3.4.0
15:56:25.856 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:25.856 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:25.856 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:25.856 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:25.856 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:25.856 INFO  Funcotator - Deflater: IntelDeflater
15:56:25.856 INFO  Funcotator - Inflater: IntelInflater
15:56:25.856 INFO  Funcotator - GCS max retries/reopens: 20
15:56:25.856 INFO  Funcotator - Requester pays: disabled
15:56:25.856 INFO  Funcotator - Initializing engine
15:56:25.858 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
15:56:25.859 INFO  Funcotator - Done initializing engine
15:56:25.859 INFO  Funcotator - Validating sequence dictionaries...
15:56:25.859 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:25.859 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:25 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:25.949 INFO  Funcotator - ------------------------------------------------------------
15:56:25.949 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:25.949 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:25.949 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:25.949 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:25.949 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:25 PM GMT
15:56:25.949 INFO  Funcotator - ------------------------------------------------------------
15:56:25.949 INFO  Funcotator - ------------------------------------------------------------
15:56:25.949 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:25.949 INFO  Funcotator - Picard Version: 3.4.0
15:56:25.949 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:25.949 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:25.949 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:25.949 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:25.949 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:25.949 INFO  Funcotator - Deflater: IntelDeflater
15:56:25.949 INFO  Funcotator - Inflater: IntelInflater
15:56:25.949 INFO  Funcotator - GCS max retries/reopens: 20
15:56:25.949 INFO  Funcotator - Requester pays: disabled
15:56:25.949 INFO  Funcotator - Initializing engine
15:56:25.951 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:56:25.972 INFO  Funcotator - Done initializing engine
15:56:25.972 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:25.972 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:25.972 INFO  Funcotator - Initializing data sources...
15:56:25.972 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:25.972 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:25.972 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
15:56:25.972 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
15:56:25.972 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
15:56:25.973 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:25.973 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
15:56:25.973 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:25.973 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
15:56:25.974 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
15:56:25.974 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
15:56:25.974 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:25.975 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
15:56:25.983 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
15:56:25.993 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
15:56:26.002 INFO  Funcotator - Initializing Funcotator Engine...
15:56:26.009 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:26.009 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9394326037565900618.vcf
15:56:26.021 INFO  ProgressMeter - Starting traversal
15:56:26.021 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:26.051 INFO  ProgressMeter -             unmapped              0.0                   100         200000.0
15:56:26.051 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:56:26.051 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:56:26.057 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:26.058 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out9394326037565900618.vcf
15:56:26.167 INFO  Funcotator - ------------------------------------------------------------
15:56:26.167 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:26.167 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:26.167 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:26.167 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:26.167 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:26 PM GMT
15:56:26.167 INFO  Funcotator - ------------------------------------------------------------
15:56:26.167 INFO  Funcotator - ------------------------------------------------------------
15:56:26.167 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:26.167 INFO  Funcotator - Picard Version: 3.4.0
15:56:26.167 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:26.167 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:26.167 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:26.167 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:26.167 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:26.167 INFO  Funcotator - Deflater: IntelDeflater
15:56:26.167 INFO  Funcotator - Inflater: IntelInflater
15:56:26.167 INFO  Funcotator - GCS max retries/reopens: 20
15:56:26.167 INFO  Funcotator - Requester pays: disabled
15:56:26.167 INFO  Funcotator - Initializing engine
15:56:26.168 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:56:26.170 INFO  Funcotator - Done initializing engine
15:56:26.170 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:26.170 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:26.170 INFO  Funcotator - Initializing data sources...
15:56:26.170 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:26.170 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:26.170 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
15:56:26.171 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
15:56:26.171 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
15:56:26.171 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:26.171 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
15:56:26.171 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:26.171 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
15:56:26.172 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
15:56:26.172 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
15:56:26.172 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:26.173 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
15:56:26.173 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
15:56:26.175 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
15:56:26.175 INFO  Funcotator - Initializing Funcotator Engine...
15:56:26.176 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:26.176 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.
15:56:26.176 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out17351508026442664986.vcf
15:56:26.179 INFO  ProgressMeter - Starting traversal
15:56:26.179 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:26.188 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
15:56:26.188 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:56:26.188 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:56:26.191 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:26.192 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out17351508026442664986.vcf
15:56:26.291 INFO  Funcotator - ------------------------------------------------------------
15:56:26.291 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:26.291 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:26.291 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:26.291 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:26.291 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:26 PM GMT
15:56:26.291 INFO  Funcotator - ------------------------------------------------------------
15:56:26.291 INFO  Funcotator - ------------------------------------------------------------
15:56:26.291 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:26.291 INFO  Funcotator - Picard Version: 3.4.0
15:56:26.291 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:26.291 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:26.291 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:26.291 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:26.291 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:26.291 INFO  Funcotator - Deflater: IntelDeflater
15:56:26.291 INFO  Funcotator - Inflater: IntelInflater
15:56:26.291 INFO  Funcotator - GCS max retries/reopens: 20
15:56:26.291 INFO  Funcotator - Requester pays: disabled
15:56:26.291 INFO  Funcotator - Initializing engine
15:56:26.293 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
15:56:26.306 INFO  Funcotator - Done initializing engine
15:56:26.306 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:26.306 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:26.306 INFO  Funcotator - Initializing data sources...
15:56:26.306 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:26.306 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:26.306 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
15:56:26.307 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
15:56:26.307 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
15:56:26.307 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:26.307 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
15:56:26.307 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:26.308 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
15:56:26.308 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
15:56:26.308 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
15:56:26.308 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:26.309 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
15:56:26.317 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
15:56:26.325 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
15:56:26.333 INFO  Funcotator - Initializing Funcotator Engine...
15:56:26.337 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:26.337 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out11482145123636901176.vcf
15:56:26.348 INFO  ProgressMeter - Starting traversal
15:56:26.348 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:26.352 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)
15:56:26.353 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)
15:56:26.353 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:26.353 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:56:26.353 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:56:26.353 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:56:26.355 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:26.355 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:56:26.355 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:56:26.355 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:56:26.356 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)
15:56:26.356 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)
15:56:26.356 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:26.357 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:56:26.357 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:56:26.357 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:56:26.357 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)
15:56:26.358 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)
15:56:26.358 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
15:56:26.358 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
15:56:26.358 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:56:26.358 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:56:26.359 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:26.359 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:56:26.359 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:56:26.359 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:56:26.360 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:26.360 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:56:26.360 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:56:26.360 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:56:26.360 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)
15:56:26.361 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)
15:56:26.361 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:56:26.361 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:56:26.361 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:56:26.361 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:56:26.362 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)
15:56:26.362 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)
15:56:26.362 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:26.362 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:56:26.362 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:56:26.362 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:56:26.363 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:56:26.363 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:56:26.363 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:56:26.363 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:56:26.364 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)
15:56:26.364 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)
15:56:26.364 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:26.364 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:56:26.364 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:56:26.364 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:56:26.365 INFO  ProgressMeter -             unmapped              0.0                    10          35294.1
15:56:26.365 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
15:56:26.365 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:56:26.370 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:26.371 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out11482145123636901176.vcf
15:56:26.473 INFO  Funcotator - ------------------------------------------------------------
15:56:26.473 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:26.473 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:26.473 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:26.473 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:26.473 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:26 PM GMT
15:56:26.473 INFO  Funcotator - ------------------------------------------------------------
15:56:26.473 INFO  Funcotator - ------------------------------------------------------------
15:56:26.473 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:26.473 INFO  Funcotator - Picard Version: 3.4.0
15:56:26.473 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:26.473 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:26.473 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:26.473 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:26.473 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:26.473 INFO  Funcotator - Deflater: IntelDeflater
15:56:26.473 INFO  Funcotator - Inflater: IntelInflater
15:56:26.473 INFO  Funcotator - GCS max retries/reopens: 20
15:56:26.473 INFO  Funcotator - Requester pays: disabled
15:56:26.473 INFO  Funcotator - Initializing engine
15:56:26.475 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/non_locatable_proof_input.vcf
15:56:26.476 INFO  Funcotator - Done initializing engine
15:56:26.476 INFO  Funcotator - Validating sequence dictionaries...
15:56:26.477 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:26.477 INFO  Funcotator - Initializing data sources...
15:56:26.477 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:26.477 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:26.477 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
15:56:26.477 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
15:56:26.477 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
15:56:26.478 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
15:56:26.478 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
15:56:26.478 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
15:56:26.478 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:26.478 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:26.479 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
15:56:26.479 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
15:56:26.479 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
15:56:26.479 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
15:56:26.479 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:26.479 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:26.480 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:56:26.480 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:26.480 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/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:56:26.480 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:56:26.499 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
15:56:26.499 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
15:56:26.545 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
15:56:26.545 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
15:56:27.118 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:27.118 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:27.119 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:27.121 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:27.124 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:27.126 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:27.126 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:27.127 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:27.161 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:27.162 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:27	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:27.162 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
15:56:27.200 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
15:56:27.201 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
15:56:27.201 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
15:56:27.209 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:27.209 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
15:56:27.209 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:27.210 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:27.210 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
15:56:27.298 INFO  Funcotator - Initializing Funcotator Engine...
15:56:27.298 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:56:27.298 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.
15:56:27.298 INFO  Funcotator - Creating a VCF file for output: file:/tmp/non_locatable_proof_input.vcf.funcotator3300505802531117720.vcf
15:56:27.302 INFO  ProgressMeter - Starting traversal
15:56:27.302 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:27.348 INFO  ProgressMeter -             unmapped              0.0                     1           1304.3
15:56:27.348 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:56:27.348 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:56:27.348 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:27 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360
15:56:27.349 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/non_locatable_proof_input.vcf.funcotator3300505802531117720.vcf
15:56:27.441 INFO  Funcotator - ------------------------------------------------------------
15:56:27.441 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:27.441 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:27.441 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:27.441 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:27.441 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:27 PM GMT
15:56:27.441 INFO  Funcotator - ------------------------------------------------------------
15:56:27.441 INFO  Funcotator - ------------------------------------------------------------
15:56:27.441 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:27.441 INFO  Funcotator - Picard Version: 3.4.0
15:56:27.441 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:27.441 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:27.441 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:27.441 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:27.441 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:27.441 INFO  Funcotator - Deflater: IntelDeflater
15:56:27.441 INFO  Funcotator - Inflater: IntelInflater
15:56:27.441 INFO  Funcotator - GCS max retries/reopens: 20
15:56:27.441 INFO  Funcotator - Requester pays: disabled
15:56:27.441 INFO  Funcotator - Initializing engine
15:56:27.443 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/symbollic_allele_proof_input.vcf
15:56:27.445 INFO  Funcotator - Done initializing engine
15:56:27.445 INFO  Funcotator - Validating sequence dictionaries...
15:56:27.445 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:27.445 INFO  Funcotator - Initializing data sources...
15:56:27.445 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:27.445 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:27.445 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
15:56:27.445 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
15:56:27.446 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
15:56:27.446 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
15:56:27.446 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
15:56:27.446 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
15:56:27.446 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:27.446 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:27.447 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
15:56:27.447 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
15:56:27.447 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
15:56:27.447 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
15:56:27.447 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:27.447 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
15:56:27.448 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
15:56:27.448 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:27.448 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
15:56:27.448 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
15:56:27.467 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
15:56:27.468 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
15:56:27.513 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
15:56:27.513 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
15:56:28.079 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:28.080 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:28.081 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:28.082 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:28.085 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:28.087 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:28.087 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:28.088 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:28.115 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:28.115 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:28	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:28.116 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
15:56:28.154 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
15:56:28.155 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
15:56:28.155 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
15:56:28.163 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:28.163 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
15:56:28.163 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:28.164 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:28.164 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
15:56:28.249 INFO  Funcotator - Initializing Funcotator Engine...
15:56:28.249 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:56:28.249 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.
15:56:28.249 INFO  Funcotator - Creating a VCF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator12652482215051260639.vcf
15:56:28.253 INFO  ProgressMeter - Starting traversal
15:56:28.253 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:28.259 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1007545-1007545 due to alternate allele: <NON_REF>
15:56:28.296 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:56:28.296 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:56:28.296 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:56:28.296 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:56:28.296 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:56:28.296 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:56:28.296 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:56:28.299 INFO  ProgressMeter -             unmapped              0.0                     2           2608.7
15:56:28.299 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:56:28.299 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:56:28.300 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:28 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360
15:56:28.301 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/symbollic_allele_proof_input.vcf.funcotator12652482215051260639.vcf
15:56:28.389 INFO  Funcotator - ------------------------------------------------------------
15:56:28.389 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:28.389 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:28.389 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:28.389 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:28.389 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:28 PM GMT
15:56:28.389 INFO  Funcotator - ------------------------------------------------------------
15:56:28.389 INFO  Funcotator - ------------------------------------------------------------
15:56:28.389 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:28.389 INFO  Funcotator - Picard Version: 3.4.0
15:56:28.389 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:28.389 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:28.390 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:28.390 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:28.390 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:28.390 INFO  Funcotator - Deflater: IntelDeflater
15:56:28.390 INFO  Funcotator - Inflater: IntelInflater
15:56:28.390 INFO  Funcotator - GCS max retries/reopens: 20
15:56:28.390 INFO  Funcotator - Requester pays: disabled
15:56:28.390 INFO  Funcotator - Initializing engine
15:56:28.392 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_input_test.vcf
15:56:28.393 INFO  Funcotator - Done initializing engine
15:56:28.393 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:28.393 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:28.393 INFO  Funcotator - Initializing data sources...
15:56:28.393 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:28.393 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:28.393 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
15:56:28.393 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
15:56:28.393 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
15:56:28.394 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
15:56:28.394 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
15:56:28.394 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
15:56:28.394 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
15:56:28.394 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
15:56:28.394 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
15:56:28.395 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
15:56:28.395 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:56:28.395 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
15:56:28.395 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:28.395 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
15:56:28.396 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
15:56:28.396 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:28.396 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
15:56:28.396 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
15:56:28.415 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
15:56:28.415 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
15:56:28.489 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
15:56:28.490 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
15:56:29.024 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:29.024 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:29.025 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:29.027 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
15:56:29.029 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:29.031 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:29.031 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:29.032 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:29.061 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:29.061 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:29	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:29.061 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
15:56:29.101 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
15:56:29.102 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:56:29.102 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
15:56:29.110 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:29.110 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
15:56:29.110 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:29.111 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:29.112 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
15:56:29.197 INFO  Funcotator - Initializing Funcotator Engine...
15:56:29.198 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:29.198 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
15:56:29.198 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
15:56:29.198 INFO  FuncotatorUtils -     Setting new Variant Classification severity: INTRON = 0
15:56:29.198 INFO  FuncotatorUtils -     Setting new Variant Classification severity: SILENT = 999
15:56:29.198 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out14077004052831983630.vcf
15:56:29.202 INFO  ProgressMeter - Starting traversal
15:56:29.202 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:29.240 INFO  ProgressMeter -             unmapped              0.0                     1           1578.9
15:56:29.240 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:56:29.240 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:56:29.240 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:29 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360
15:56:29.241 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out14077004052831983630.vcf
15:56:29.242 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_expected_out.vcf
[May 27, 2025 at 3:56:29 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:56:29 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:29.562 INFO  Funcotator - ------------------------------------------------------------
15:56:29.562 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:29.562 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:29.562 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:29.562 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:29.562 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:29 PM GMT
15:56:29.563 INFO  Funcotator - ------------------------------------------------------------
15:56:29.563 INFO  Funcotator - ------------------------------------------------------------
15:56:29.563 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:29.563 INFO  Funcotator - Picard Version: 3.4.0
15:56:29.563 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:29.563 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:29.563 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:29.563 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:29.563 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:29.563 INFO  Funcotator - Deflater: IntelDeflater
15:56:29.563 INFO  Funcotator - Inflater: IntelInflater
15:56:29.563 INFO  Funcotator - GCS max retries/reopens: 20
15:56:29.563 INFO  Funcotator - Requester pays: disabled
15:56:29.563 INFO  Funcotator - Initializing engine
15:56:29.564 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:56:29.581 INFO  Funcotator - Done initializing engine
15:56:29.581 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:29.581 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:29.581 INFO  Funcotator - Initializing data sources...
15:56:29.581 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:29.581 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:29.581 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
15:56:29.581 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
15:56:29.581 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg38_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
15:56:29.581 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:29.581 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
15:56:29.581 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:29.582 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
15:56:29.582 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg38/gencode.v28.PIK3CA_transcript.fasta
15:56:29.583 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
15:56:29.583 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:29.583 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
15:56:29.591 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
15:56:29.600 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
15:56:29.608 INFO  Funcotator - Initializing Funcotator Engine...
15:56:29.614 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:29.614 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out441744016696157007.vcf
15:56:29.627 INFO  ProgressMeter - Starting traversal
15:56:29.627 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:29.654 INFO  ProgressMeter -             unmapped              0.0                   100         222222.2
15:56:29.654 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:56:29.654 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:56:29.660 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:29 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:29.661 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out441744016696157007.vcf
15:56:29.768 INFO  Funcotator - ------------------------------------------------------------
15:56:29.769 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:29.769 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:29.769 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:29.769 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:29.769 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:29 PM GMT
15:56:29.769 INFO  Funcotator - ------------------------------------------------------------
15:56:29.769 INFO  Funcotator - ------------------------------------------------------------
15:56:29.769 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:29.769 INFO  Funcotator - Picard Version: 3.4.0
15:56:29.769 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:29.769 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:29.769 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:29.769 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:29.769 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:29.769 INFO  Funcotator - Deflater: IntelDeflater
15:56:29.769 INFO  Funcotator - Inflater: IntelInflater
15:56:29.769 INFO  Funcotator - GCS max retries/reopens: 20
15:56:29.769 INFO  Funcotator - Requester pays: disabled
15:56:29.769 INFO  Funcotator - Initializing engine
15:56:29.771 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/FILTER_test.vcf
15:56:29.772 INFO  Funcotator - Done initializing engine
15:56:29.772 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:29.772 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:29.772 INFO  Funcotator - Initializing data sources...
15:56:29.772 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/
15:56:29.772 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:29.772 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
15:56:29.773 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
15:56:29.773 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
15:56:29.773 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:29.773 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
15:56:29.773 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
15:56:29.773 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
15:56:29.775 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
15:56:29.778 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
15:56:29.780 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
15:56:29.780 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:29.781 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
15:56:29.781 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
15:56:29.781 INFO  Funcotator - Initializing Funcotator Engine...
15:56:29.782 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:29.782 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.
15:56:29.782 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:29.782 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing10748751295407365414.vcf
15:56:29.784 INFO  ProgressMeter - Starting traversal
15:56:29.784 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:29.805 INFO  ProgressMeter -             unmapped              0.0                     1           2857.1
15:56:29.806 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:56:29.806 INFO  VcfFuncotationFactory - dbSnp 9606_b150 cache hits/total: 0/1
15:56:29.808 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:29 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:29.809 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing10748751295407365414.vcf
15:56:29.901 INFO  Funcotator - ------------------------------------------------------------
15:56:29.901 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:29.901 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:29.901 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:29.901 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:29.901 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:29 PM GMT
15:56:29.901 INFO  Funcotator - ------------------------------------------------------------
15:56:29.901 INFO  Funcotator - ------------------------------------------------------------
15:56:29.901 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:29.901 INFO  Funcotator - Picard Version: 3.4.0
15:56:29.901 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:29.901 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:29.901 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:29.901 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:29.901 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:29.901 INFO  Funcotator - Deflater: IntelDeflater
15:56:29.901 INFO  Funcotator - Inflater: IntelInflater
15:56:29.901 INFO  Funcotator - GCS max retries/reopens: 20
15:56:29.901 INFO  Funcotator - Requester pays: disabled
15:56:29.901 INFO  Funcotator - Initializing engine
15:56:29.902 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:56:29.903 INFO  Funcotator - Done initializing engine
15:56:29.903 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:29.903 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:29.903 INFO  Funcotator - Initializing data sources...
15:56:29.903 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:29.903 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:29.903 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
15:56:29.904 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
15:56:29.904 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
15:56:29.904 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
15:56:29.904 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:56:29.904 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
15:56:29.905 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:29.905 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:29.905 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
15:56:29.905 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:56:29.905 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:56:29.906 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:56:29.906 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:29.906 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
15:56:29.906 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
15:56:29.906 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:29.906 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
15:56:29.906 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
15:56:29.925 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
15:56:29.926 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
15:56:29.971 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
15:56:29.972 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
15:56:30.537 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:30.537 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:30.538 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:30.539 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:30.542 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:30.544 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:30.545 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:30.545 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:30.572 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
15:56:30.573 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:30	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:30.573 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
15:56:30.612 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
15:56:30.612 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
15:56:30.612 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:56:30.620 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:30.620 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
15:56:30.620 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:30.621 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:30.621 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:56:30.707 INFO  Funcotator - Initializing Funcotator Engine...
15:56:30.707 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
15:56:30.707 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:56:30.707 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:56:30.707 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:56:30.707 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:56:30.708 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:56:30.708 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:30.708 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3909103365239738759.vcf
15:56:30.708 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
15:56:30.710 INFO  ProgressMeter - Starting traversal
15:56:30.710 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:30.731 INFO  ProgressMeter -             unmapped              0.0                     3           8571.4
15:56:30.731 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:56:30.731 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:56:30.734 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:30 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360
15:56:30.830 INFO  Funcotator - ------------------------------------------------------------
15:56:30.830 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:30.830 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:30.830 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:30.830 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:30.831 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:30 PM GMT
15:56:30.831 INFO  Funcotator - ------------------------------------------------------------
15:56:30.831 INFO  Funcotator - ------------------------------------------------------------
15:56:30.831 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:30.831 INFO  Funcotator - Picard Version: 3.4.0
15:56:30.831 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:30.831 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:30.831 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:30.831 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:30.831 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:30.831 INFO  Funcotator - Deflater: IntelDeflater
15:56:30.831 INFO  Funcotator - Inflater: IntelInflater
15:56:30.831 INFO  Funcotator - GCS max retries/reopens: 20
15:56:30.831 INFO  Funcotator - Requester pays: disabled
15:56:30.831 INFO  Funcotator - Initializing engine
15:56:30.832 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:56:30.833 INFO  Funcotator - Done initializing engine
15:56:30.833 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:30.833 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:30.833 INFO  Funcotator - Initializing data sources...
15:56:30.833 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:30.833 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:30.833 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
15:56:30.833 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
15:56:30.834 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:56:30.834 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:56:30.834 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
15:56:30.834 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
15:56:30.834 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:30.835 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:30.835 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:56:30.835 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
15:56:30.835 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
15:56:30.835 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
15:56:30.835 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:30.836 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
15:56:30.836 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
15:56:30.836 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:30.836 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
15:56:30.836 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
15:56:30.861 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
15:56:30.862 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
15:56:30.907 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
15:56:30.907 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
15:56:31.473 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:31.473 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:31.474 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:31.476 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:31.478 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:31.481 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:31.481 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:31.481 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:31.509 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:31.509 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:31	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:31.509 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
15:56:31.548 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
15:56:31.549 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
15:56:31.549 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
15:56:31.557 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:31.557 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
15:56:31.557 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:31.558 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:31.558 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
15:56:31.644 INFO  Funcotator - Initializing Funcotator Engine...
15:56:31.644 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:31.644 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:31.644 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13032130578892431832.vcf
15:56:31.645 INFO  ProgressMeter - Starting traversal
15:56:31.645 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:31.744 INFO  ProgressMeter -             unmapped              0.0                     4           2424.2
15:56:31.744 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:56:31.745 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:56:31.745 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:31 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3261071360
15:56:31.839 INFO  Funcotator - ------------------------------------------------------------
15:56:31.839 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:31.839 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:31.839 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:31.839 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:31.839 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:31 PM GMT
15:56:31.839 INFO  Funcotator - ------------------------------------------------------------
15:56:31.839 INFO  Funcotator - ------------------------------------------------------------
15:56:31.840 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:31.840 INFO  Funcotator - Picard Version: 3.4.0
15:56:31.840 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:31.840 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:31.840 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:31.840 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:31.840 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:31.840 INFO  Funcotator - Deflater: IntelDeflater
15:56:31.840 INFO  Funcotator - Inflater: IntelInflater
15:56:31.840 INFO  Funcotator - GCS max retries/reopens: 20
15:56:31.840 INFO  Funcotator - Requester pays: disabled
15:56:31.840 INFO  Funcotator - Initializing engine
15:56:31.840 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:56:31.841 INFO  Funcotator - Done initializing engine
15:56:31.841 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:31.841 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:31.841 INFO  Funcotator - Initializing data sources...
15:56:31.841 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:31.841 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:31.842 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
15:56:31.842 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
15:56:31.842 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
15:56:31.842 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
15:56:31.842 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
15:56:31.842 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
15:56:31.843 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:31.843 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:31.843 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
15:56:31.843 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
15:56:31.843 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
15:56:31.843 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
15:56:31.844 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:31.844 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
15:56:31.844 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
15:56:31.844 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:31.844 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
15:56:31.844 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
15:56:31.863 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
15:56:31.864 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
15:56:31.909 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
15:56:31.910 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
15:56:32.475 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:32.475 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:32.476 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:32.478 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:32.481 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:32.483 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:32.484 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:32.484 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:32.511 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:32.512 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:32	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:32.512 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
15:56:32.551 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
15:56:32.551 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
15:56:32.551 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
15:56:32.559 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:32.560 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
15:56:32.560 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:32.561 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:32.561 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
15:56:32.658 INFO  Funcotator - Initializing Funcotator Engine...
15:56:32.658 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
15:56:32.659 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:56:32.659 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:56:32.659 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:56:32.659 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:56:32.659 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:32.659 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out5778106747073581629.vcf
15:56:32.660 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
15:56:32.661 INFO  ProgressMeter - Starting traversal
15:56:32.661 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:32.685 INFO  ProgressMeter -             unmapped              0.0                     3           7500.0
15:56:32.685 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:56:32.685 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:56:32.688 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:32 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360
15:56:32.782 INFO  Funcotator - ------------------------------------------------------------
15:56:32.782 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:32.782 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:32.782 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:32.782 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:32.782 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:32 PM GMT
15:56:32.782 INFO  Funcotator - ------------------------------------------------------------
15:56:32.782 INFO  Funcotator - ------------------------------------------------------------
15:56:32.782 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:32.782 INFO  Funcotator - Picard Version: 3.4.0
15:56:32.782 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:32.782 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:32.782 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:32.782 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:32.782 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:32.782 INFO  Funcotator - Deflater: IntelDeflater
15:56:32.782 INFO  Funcotator - Inflater: IntelInflater
15:56:32.782 INFO  Funcotator - GCS max retries/reopens: 20
15:56:32.782 INFO  Funcotator - Requester pays: disabled
15:56:32.782 INFO  Funcotator - Initializing engine
15:56:32.783 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:56:32.784 INFO  Funcotator - Done initializing engine
15:56:32.784 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:32.784 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:32.784 INFO  Funcotator - Initializing data sources...
15:56:32.784 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:32.784 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:32.784 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
15:56:32.785 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:56:32.785 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
15:56:32.785 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
15:56:32.785 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
15:56:32.785 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:56:32.786 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
15:56:32.786 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:32.786 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
15:56:32.786 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
15:56:32.786 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
15:56:32.786 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
15:56:32.787 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:32.787 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
15:56:32.787 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
15:56:32.787 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:32.787 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
15:56:32.787 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
15:56:32.810 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
15:56:32.810 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
15:56:32.885 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
15:56:32.885 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:56:33.420 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:33.420 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:33.421 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:33.423 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
15:56:33.426 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:33.428 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:33.428 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:33.428 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:33.456 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:33.456 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:33	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:33.456 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
15:56:33.495 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
15:56:33.495 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
15:56:33.496 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
15:56:33.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:33.504 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
15:56:33.504 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:33.505 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:33.505 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
15:56:33.592 INFO  Funcotator - Initializing Funcotator Engine...
15:56:33.592 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:33.592 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:33.593 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4242156320089689448.vcf
15:56:33.595 INFO  ProgressMeter - Starting traversal
15:56:33.595 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:33.704 INFO  ProgressMeter -             unmapped              0.0                     4           2201.8
15:56:33.704 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:56:33.704 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:56:33.704 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:33 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3261071360
15:56:33.808 INFO  Funcotator - ------------------------------------------------------------
15:56:33.808 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:33.808 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:33.808 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:33.808 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:33.808 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:33 PM GMT
15:56:33.808 INFO  Funcotator - ------------------------------------------------------------
15:56:33.808 INFO  Funcotator - ------------------------------------------------------------
15:56:33.808 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:33.808 INFO  Funcotator - Picard Version: 3.4.0
15:56:33.808 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:33.808 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:33.808 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:33.808 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:33.808 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:33.808 INFO  Funcotator - Deflater: IntelDeflater
15:56:33.808 INFO  Funcotator - Inflater: IntelInflater
15:56:33.808 INFO  Funcotator - GCS max retries/reopens: 20
15:56:33.808 INFO  Funcotator - Requester pays: disabled
15:56:33.808 INFO  Funcotator - Initializing engine
15:56:33.809 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:56:33.810 INFO  Funcotator - Done initializing engine
15:56:33.810 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:33.810 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:33.810 INFO  Funcotator - Initializing data sources...
15:56:33.810 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:33.810 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:33.811 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
15:56:33.811 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
15:56:33.811 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
15:56:33.811 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
15:56:33.811 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
15:56:33.812 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
15:56:33.812 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:33.812 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:33.812 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
15:56:33.812 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
15:56:33.813 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
15:56:33.813 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
15:56:33.813 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:33.813 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
15:56:33.813 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
15:56:33.813 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:33.813 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:56:33.814 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:56:33.837 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
15:56:33.837 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
15:56:33.883 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
15:56:33.883 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
15:56:34.419 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:34.419 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:34.420 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:34.422 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:34.425 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:34.427 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:34.427 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:34.428 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:34.455 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:34.456 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:34	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:34.456 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
15:56:34.495 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
15:56:34.496 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
15:56:34.496 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
15:56:34.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:34.505 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
15:56:34.505 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:34.506 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:34.506 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
15:56:34.591 INFO  Funcotator - Initializing Funcotator Engine...
15:56:34.591 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
15:56:34.591 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:56:34.591 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:56:34.591 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:56:34.591 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:56:34.592 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:56:34.592 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:34.592 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out12312823989980951449.maf
15:56:34.593 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
15:56:34.593 INFO  ProgressMeter - Starting traversal
15:56:34.594 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:34.617 INFO  ProgressMeter -             unmapped              0.0                     3           7826.1
15:56:34.617 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:56:34.617 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:56:34.618 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:34 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360
15:56:34.720 INFO  Funcotator - ------------------------------------------------------------
15:56:34.720 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:34.720 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:34.720 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:34.720 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:34.720 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:34 PM GMT
15:56:34.720 INFO  Funcotator - ------------------------------------------------------------
15:56:34.720 INFO  Funcotator - ------------------------------------------------------------
15:56:34.720 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:34.720 INFO  Funcotator - Picard Version: 3.4.0
15:56:34.720 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:34.720 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:34.720 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:34.720 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:34.720 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:34.720 INFO  Funcotator - Deflater: IntelDeflater
15:56:34.720 INFO  Funcotator - Inflater: IntelInflater
15:56:34.720 INFO  Funcotator - GCS max retries/reopens: 20
15:56:34.720 INFO  Funcotator - Requester pays: disabled
15:56:34.720 INFO  Funcotator - Initializing engine
15:56:34.721 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:56:34.722 INFO  Funcotator - Done initializing engine
15:56:34.722 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:34.722 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:34.722 INFO  Funcotator - Initializing data sources...
15:56:34.722 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:34.722 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:34.722 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
15:56:34.722 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
15:56:34.722 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
15:56:34.723 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
15:56:34.723 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
15:56:34.723 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
15:56:34.723 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:34.723 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:34.723 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
15:56:34.724 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
15:56:34.724 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
15:56:34.724 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
15:56:34.724 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:34.724 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
15:56:34.724 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:56:34.724 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:34.724 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
15:56:34.725 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
15:56:34.744 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
15:56:34.744 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
15:56:34.790 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
15:56:34.790 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
15:56:35.335 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:35.335 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:35.336 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:35.338 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:35.341 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:35.343 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:35.344 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:35.344 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:35.374 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:35.374 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:35	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:35.375 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:56:35.414 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
15:56:35.414 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
15:56:35.414 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
15:56:35.427 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:35.428 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
15:56:35.428 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:35.429 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:35.429 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
15:56:35.513 INFO  Funcotator - Initializing Funcotator Engine...
15:56:35.513 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:35.513 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:35.513 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out585089524016553134.maf
15:56:35.514 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
15:56:35.514 INFO  ProgressMeter - Starting traversal
15:56:35.514 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:35.631 INFO  ProgressMeter -             unmapped              0.0                     4           2051.3
15:56:35.631 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:56:35.631 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:56:35.631 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:35 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3261071360
15:56:35.724 INFO  Funcotator - ------------------------------------------------------------
15:56:35.724 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:35.724 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:35.724 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:35.724 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:35.724 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:35 PM GMT
15:56:35.724 INFO  Funcotator - ------------------------------------------------------------
15:56:35.724 INFO  Funcotator - ------------------------------------------------------------
15:56:35.724 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:35.724 INFO  Funcotator - Picard Version: 3.4.0
15:56:35.724 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:35.724 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:35.724 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:35.724 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:35.724 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:35.724 INFO  Funcotator - Deflater: IntelDeflater
15:56:35.724 INFO  Funcotator - Inflater: IntelInflater
15:56:35.724 INFO  Funcotator - GCS max retries/reopens: 20
15:56:35.724 INFO  Funcotator - Requester pays: disabled
15:56:35.724 INFO  Funcotator - Initializing engine
15:56:35.725 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:56:35.726 INFO  Funcotator - Done initializing engine
15:56:35.726 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:35.726 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:35.726 INFO  Funcotator - Initializing data sources...
15:56:35.726 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:35.726 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:35.726 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
15:56:35.726 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
15:56:35.726 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
15:56:35.727 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
15:56:35.727 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
15:56:35.727 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
15:56:35.727 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
15:56:35.727 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
15:56:35.727 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
15:56:35.727 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
15:56:35.728 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
15:56:35.728 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
15:56:35.728 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:35.728 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
15:56:35.728 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
15:56:35.728 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:35.728 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
15:56:35.728 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
15:56:35.748 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
15:56:35.748 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
15:56:35.793 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
15:56:35.794 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
15:56:36.336 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:36.336 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:36.337 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:36.339 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:36.342 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:36.344 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:36.344 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:36.345 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:36.372 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:36.373 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:36	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:36.373 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
15:56:36.412 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
15:56:36.412 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
15:56:36.412 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
15:56:36.420 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:36.420 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
15:56:36.420 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:36.421 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:36.421 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
15:56:36.507 INFO  Funcotator - Initializing Funcotator Engine...
15:56:36.507 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
15:56:36.507 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:56:36.507 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:56:36.507 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:56:36.507 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:56:36.508 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:56:36.508 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:56:36.508 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:56:36.508 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:56:36.508 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:36.508 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5298061363629023370.maf
15:56:36.508 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
15:56:36.508 INFO  ProgressMeter - Starting traversal
15:56:36.508 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:36.526 INFO  ProgressMeter -             unmapped              0.0                     3          10000.0
15:56:36.526 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:56:36.526 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:56:36.526 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:36 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360
15:56:36.617 INFO  Funcotator - ------------------------------------------------------------
15:56:36.617 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:36.617 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:36.617 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:36.617 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:36.617 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:36 PM GMT
15:56:36.617 INFO  Funcotator - ------------------------------------------------------------
15:56:36.617 INFO  Funcotator - ------------------------------------------------------------
15:56:36.618 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:36.618 INFO  Funcotator - Picard Version: 3.4.0
15:56:36.618 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:36.618 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:36.618 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:36.618 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:36.618 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:36.618 INFO  Funcotator - Deflater: IntelDeflater
15:56:36.618 INFO  Funcotator - Inflater: IntelInflater
15:56:36.618 INFO  Funcotator - GCS max retries/reopens: 20
15:56:36.618 INFO  Funcotator - Requester pays: disabled
15:56:36.618 INFO  Funcotator - Initializing engine
15:56:36.619 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:56:36.619 INFO  Funcotator - Done initializing engine
15:56:36.619 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:36.619 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:36.619 INFO  Funcotator - Initializing data sources...
15:56:36.619 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:36.619 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:36.620 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
15:56:36.620 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
15:56:36.620 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
15:56:36.620 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
15:56:36.620 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
15:56:36.620 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
15:56:36.620 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
15:56:36.620 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
15:56:36.621 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
15:56:36.621 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
15:56:36.621 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
15:56:36.621 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
15:56:36.621 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:36.621 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
15:56:36.621 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:56:36.621 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:36.621 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
15:56:36.622 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
15:56:36.648 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
15:56:36.648 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
15:56:36.693 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
15:56:36.694 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
15:56:37.231 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:37.231 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:37.232 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:37.234 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:37.237 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:37.239 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:37.239 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:37.240 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:37.267 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:37.267 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:37	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:37.268 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
15:56:37.307 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
15:56:37.307 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
15:56:37.307 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
15:56:37.315 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:37.316 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
15:56:37.316 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:37.316 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:37.317 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
15:56:37.402 INFO  Funcotator - Initializing Funcotator Engine...
15:56:37.403 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:37.403 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:37.403 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out9487617866330734060.maf
15:56:37.403 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
15:56:37.403 INFO  ProgressMeter - Starting traversal
15:56:37.403 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:37.499 INFO  ProgressMeter -             unmapped              0.0                     4           2500.0
15:56:37.499 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:56:37.499 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:56:37.499 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:37 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360
15:56:37.588 INFO  Funcotator - ------------------------------------------------------------
15:56:37.588 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:37.588 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:37.588 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:37.588 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:37.588 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:37 PM GMT
15:56:37.588 INFO  Funcotator - ------------------------------------------------------------
15:56:37.588 INFO  Funcotator - ------------------------------------------------------------
15:56:37.588 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:37.588 INFO  Funcotator - Picard Version: 3.4.0
15:56:37.588 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:37.588 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:37.588 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:37.588 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:37.588 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:37.588 INFO  Funcotator - Deflater: IntelDeflater
15:56:37.588 INFO  Funcotator - Inflater: IntelInflater
15:56:37.588 INFO  Funcotator - GCS max retries/reopens: 20
15:56:37.588 INFO  Funcotator - Requester pays: disabled
15:56:37.588 INFO  Funcotator - Initializing engine
15:56:37.589 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:56:37.613 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
15:56:37.613 INFO  Funcotator - Done initializing engine
15:56:37.613 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:37.613 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:37.613 INFO  Funcotator - Initializing data sources...
15:56:37.613 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
15:56:37.613 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:37.613 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
15:56:37.613 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
15:56:37.614 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
15:56:37.614 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:37.614 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
15:56:37.614 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:37.614 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
15:56:37.622 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
15:56:37.630 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
15:56:37.645 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
15:56:37.645 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:37.646 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
15:56:37.646 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
15:56:37.647 INFO  Funcotator - Initializing Funcotator Engine...
15:56:37.650 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:37.650 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out2061831269704519802.vcf
15:56:37.662 INFO  ProgressMeter - Starting traversal
15:56:37.662 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:37.674 INFO  ProgressMeter -             unmapped              0.0                    32         160000.0
15:56:37.674 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
15:56:37.674 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:56:37.679 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:37 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:37.773 INFO  Funcotator - ------------------------------------------------------------
15:56:37.773 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:37.773 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:37.773 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:37.773 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:37.773 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:37 PM GMT
15:56:37.773 INFO  Funcotator - ------------------------------------------------------------
15:56:37.773 INFO  Funcotator - ------------------------------------------------------------
15:56:37.773 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:37.773 INFO  Funcotator - Picard Version: 3.4.0
15:56:37.773 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:37.773 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:37.773 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:37.773 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:37.773 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:37.773 INFO  Funcotator - Deflater: IntelDeflater
15:56:37.773 INFO  Funcotator - Inflater: IntelInflater
15:56:37.773 INFO  Funcotator - GCS max retries/reopens: 20
15:56:37.773 INFO  Funcotator - Requester pays: disabled
15:56:37.773 INFO  Funcotator - Initializing engine
15:56:37.774 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:56:37.796 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
15:56:37.796 INFO  Funcotator - Done initializing engine
15:56:37.796 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:37.796 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:37.796 INFO  Funcotator - Initializing data sources...
15:56:37.796 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
15:56:37.796 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:37.796 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
15:56:37.797 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
15:56:37.797 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
15:56:37.797 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:37.797 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
15:56:37.797 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:37.798 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
15:56:37.805 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
15:56:37.814 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
15:56:37.821 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
15:56:37.821 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:37.822 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
15:56:37.822 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
15:56:37.823 INFO  Funcotator - Initializing Funcotator Engine...
15:56:37.827 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:37.827 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out5876397828155774262.vcf
15:56:37.840 INFO  ProgressMeter - Starting traversal
15:56:37.840 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:37.853 INFO  ProgressMeter -             unmapped              0.0                    32         147692.3
15:56:37.853 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
15:56:37.853 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:56:37.859 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:37 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:37.859 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out2061831269704519802.vcf
15:56:37.869 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out5876397828155774262.vcf
15:56:37.982 INFO  Funcotator - ------------------------------------------------------------
15:56:37.982 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:37.982 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:37.982 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:37.982 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:37.982 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:37 PM GMT
15:56:37.982 INFO  Funcotator - ------------------------------------------------------------
15:56:37.982 INFO  Funcotator - ------------------------------------------------------------
15:56:37.982 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:37.982 INFO  Funcotator - Picard Version: 3.4.0
15:56:37.982 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:37.982 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:37.982 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:37.982 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:37.982 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:37.982 INFO  Funcotator - Deflater: IntelDeflater
15:56:37.982 INFO  Funcotator - Inflater: IntelInflater
15:56:37.982 INFO  Funcotator - GCS max retries/reopens: 20
15:56:37.982 INFO  Funcotator - Requester pays: disabled
15:56:37.982 INFO  Funcotator - Initializing engine
15:56:37.984 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf
15:56:37.986 INFO  Funcotator - Done initializing engine
15:56:37.986 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:37.986 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:37.986 INFO  Funcotator - Initializing data sources...
15:56:37.986 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:37.986 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:37.986 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
15:56:37.986 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
15:56:37.987 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
15:56:37.987 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:37.987 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
15:56:37.987 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:37.987 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
15:56:37.988 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
15:56:37.988 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
15:56:37.988 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:37.989 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
15:56:37.990 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
15:56:37.991 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
15:56:37.992 INFO  Funcotator - Initializing Funcotator Engine...
15:56:37.992 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:37.992 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.
15:56:37.992 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out11291463844311299971.maf
15:56:37.993 INFO  ProgressMeter - Starting traversal
15:56:37.993 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:37.994 WARN  MafOutputRenderer - 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
15:56:37.995 WARN  MafOutputRenderer - 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
15:56:37.995 WARN  MafOutputRenderer - 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
15:56:37.996 WARN  MafOutputRenderer - 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=
15:56:37.997 WARN  MafOutputRenderer - 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=
15:56:37.998 WARN  MafOutputRenderer - 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=
15:56:37.998 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
15:56:37.998 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:56:37.998 WARN  Funcotator - ================================================================================
15:56:37.998 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:56:37.998 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:56:37.999 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:56:37.999 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:56:37.999 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:56:37.999 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:56:37.999 WARN  Funcotator - --------------------------------------------------------------------------------
15:56:37.999 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:56:37.999 WARN  Funcotator -  run was misconfigured.     
15:56:37.999 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:56:37.999 WARN  Funcotator - ================================================================================
15:56:37.999 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:56:37.999 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:37 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:38.094 INFO  Funcotator - ------------------------------------------------------------
15:56:38.094 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:38.095 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:38.095 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:38.095 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:38.095 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:38 PM GMT
15:56:38.095 INFO  Funcotator - ------------------------------------------------------------
15:56:38.095 INFO  Funcotator - ------------------------------------------------------------
15:56:38.095 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:38.095 INFO  Funcotator - Picard Version: 3.4.0
15:56:38.095 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:38.095 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:38.095 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:38.095 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:38.095 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:38.095 INFO  Funcotator - Deflater: IntelDeflater
15:56:38.095 INFO  Funcotator - Inflater: IntelInflater
15:56:38.095 INFO  Funcotator - GCS max retries/reopens: 20
15:56:38.095 INFO  Funcotator - Requester pays: disabled
15:56:38.095 INFO  Funcotator - Initializing engine
15:56:38.096 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf
15:56:38.097 INFO  Funcotator - Done initializing engine
15:56:38.097 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:38.097 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:38.097 INFO  Funcotator - Initializing data sources...
15:56:38.097 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:38.097 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:38.097 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
15:56:38.097 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
15:56:38.097 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
15:56:38.098 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:38.098 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
15:56:38.098 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:38.098 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
15:56:38.098 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
15:56:38.099 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
15:56:38.099 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:38.099 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
15:56:38.100 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
15:56:38.101 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
15:56:38.102 INFO  Funcotator - Initializing Funcotator Engine...
15:56:38.102 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:38.102 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.
15:56:38.102 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out17744635293830357830.maf
15:56:38.103 INFO  ProgressMeter - Starting traversal
15:56:38.103 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:38.104 WARN  MafOutputRenderer - 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
15:56:38.105 WARN  MafOutputRenderer - 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
15:56:38.105 WARN  MafOutputRenderer - 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
15:56:38.107 WARN  MafOutputRenderer - 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=
15:56:38.107 WARN  MafOutputRenderer - 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=
15:56:38.109 WARN  MafOutputRenderer - 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=
15:56:38.109 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
15:56:38.109 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:56:38.109 WARN  Funcotator - ================================================================================
15:56:38.109 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:56:38.109 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:56:38.109 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:56:38.109 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:56:38.109 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:56:38.109 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:56:38.109 WARN  Funcotator - --------------------------------------------------------------------------------
15:56:38.109 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:56:38.109 WARN  Funcotator -  run was misconfigured.     
15:56:38.109 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:56:38.109 WARN  Funcotator - ================================================================================
15:56:38.109 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:56:38.109 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:38 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:38.202 INFO  Funcotator - ------------------------------------------------------------
15:56:38.203 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:38.203 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:38.203 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:38.203 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:38.203 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:38 PM GMT
15:56:38.203 INFO  Funcotator - ------------------------------------------------------------
15:56:38.203 INFO  Funcotator - ------------------------------------------------------------
15:56:38.203 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:38.203 INFO  Funcotator - Picard Version: 3.4.0
15:56:38.203 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:38.203 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:38.203 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:38.203 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:38.203 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:38.203 INFO  Funcotator - Deflater: IntelDeflater
15:56:38.203 INFO  Funcotator - Inflater: IntelInflater
15:56:38.203 INFO  Funcotator - GCS max retries/reopens: 20
15:56:38.203 INFO  Funcotator - Requester pays: disabled
15:56:38.203 INFO  Funcotator - Initializing engine
15:56:38.204 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
15:56:38.205 INFO  Funcotator - Done initializing engine
15:56:38.205 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:38.205 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:38.205 INFO  Funcotator - Initializing data sources...
15:56:38.205 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:38.205 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:38.205 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
15:56:38.205 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
15:56:38.205 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
15:56:38.205 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:38.205 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
15:56:38.205 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:38.206 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
15:56:38.206 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
15:56:38.207 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
15:56:38.207 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:38.207 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
15:56:38.208 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
15:56:38.209 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
15:56:38.210 INFO  Funcotator - Initializing Funcotator Engine...
15:56:38.210 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:38.210 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.
15:56:38.210 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out16871902026832799764.maf
15:56:38.210 INFO  ProgressMeter - Starting traversal
15:56:38.210 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:38.212 WARN  MafOutputRenderer - 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
15:56:38.212 WARN  MafOutputRenderer - 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
15:56:38.213 WARN  MafOutputRenderer - 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
15:56:38.214 WARN  MafOutputRenderer - 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=
15:56:38.214 WARN  MafOutputRenderer - 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=
15:56:38.215 WARN  MafOutputRenderer - 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=
15:56:38.215 INFO  ProgressMeter -             unmapped              0.0                     6          90000.0
15:56:38.215 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:56:38.215 WARN  Funcotator - ================================================================================
15:56:38.215 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:56:38.215 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:56:38.216 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:56:38.216 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:56:38.216 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:56:38.216 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:56:38.216 WARN  Funcotator - --------------------------------------------------------------------------------
15:56:38.216 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:56:38.216 WARN  Funcotator -  run was misconfigured.     
15:56:38.216 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:56:38.216 WARN  Funcotator - ================================================================================
15:56:38.216 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:56:38.216 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:38 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:38.309 INFO  Funcotator - ------------------------------------------------------------
15:56:38.309 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:38.309 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:38.309 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:38.309 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:38.309 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:38 PM GMT
15:56:38.309 INFO  Funcotator - ------------------------------------------------------------
15:56:38.309 INFO  Funcotator - ------------------------------------------------------------
15:56:38.309 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:38.309 INFO  Funcotator - Picard Version: 3.4.0
15:56:38.309 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:38.309 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:38.309 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:38.309 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:38.309 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:38.309 INFO  Funcotator - Deflater: IntelDeflater
15:56:38.309 INFO  Funcotator - Inflater: IntelInflater
15:56:38.309 INFO  Funcotator - GCS max retries/reopens: 20
15:56:38.309 INFO  Funcotator - Requester pays: disabled
15:56:38.309 INFO  Funcotator - Initializing engine
15:56:38.310 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
15:56:38.311 INFO  Funcotator - Done initializing engine
15:56:38.311 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:38.311 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:38.311 INFO  Funcotator - Initializing data sources...
15:56:38.311 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:38.311 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:38.312 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
15:56:38.312 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
15:56:38.312 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
15:56:38.312 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:38.312 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
15:56:38.312 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:38.312 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
15:56:38.313 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
15:56:38.313 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
15:56:38.313 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:38.314 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
15:56:38.314 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
15:56:38.316 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
15:56:38.317 INFO  Funcotator - Initializing Funcotator Engine...
15:56:38.317 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:38.317 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.
15:56:38.317 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out14489497761887915222.maf
15:56:38.317 INFO  ProgressMeter - Starting traversal
15:56:38.317 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:38.318 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
15:56:38.319 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
15:56:38.319 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
15:56:38.320 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:56:38.321 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:56:38.322 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:56:38.322 INFO  ProgressMeter -             unmapped              0.0                     6          72000.0
15:56:38.322 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:56:38.322 WARN  Funcotator - ================================================================================
15:56:38.322 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:56:38.322 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:56:38.322 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:56:38.322 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:56:38.322 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:56:38.322 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:56:38.322 WARN  Funcotator - --------------------------------------------------------------------------------
15:56:38.322 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:56:38.322 WARN  Funcotator -  run was misconfigured.     
15:56:38.322 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:56:38.322 WARN  Funcotator - ================================================================================
15:56:38.322 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:56:38.322 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:38 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:38.418 INFO  Funcotator - ------------------------------------------------------------
15:56:38.418 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:38.418 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:38.418 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:38.418 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:38.418 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:38 PM GMT
15:56:38.418 INFO  Funcotator - ------------------------------------------------------------
15:56:38.418 INFO  Funcotator - ------------------------------------------------------------
15:56:38.418 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:38.418 INFO  Funcotator - Picard Version: 3.4.0
15:56:38.418 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:38.418 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:38.418 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:38.418 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:38.418 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:38.418 INFO  Funcotator - Deflater: IntelDeflater
15:56:38.418 INFO  Funcotator - Inflater: IntelInflater
15:56:38.418 INFO  Funcotator - GCS max retries/reopens: 20
15:56:38.418 INFO  Funcotator - Requester pays: disabled
15:56:38.418 INFO  Funcotator - Initializing engine
15:56:38.419 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:56:38.421 INFO  Funcotator - Done initializing engine
15:56:38.421 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:38.421 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:38.421 INFO  Funcotator - Initializing data sources...
15:56:38.421 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:38.421 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:38.421 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
15:56:38.421 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
15:56:38.421 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:56:38.421 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:38.421 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
15:56:38.421 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:38.422 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
15:56:38.422 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
15:56:38.422 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
15:56:38.422 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:38.423 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
15:56:38.424 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:56:38.425 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
15:56:38.426 INFO  Funcotator - Initializing Funcotator Engine...
15:56:38.426 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:38.426 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.
15:56:38.426 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12333175762834823101.vcf
15:56:38.430 INFO  ProgressMeter - Starting traversal
15:56:38.430 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:38.440 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
15:56:38.440 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:56:38.440 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:56:38.443 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:38 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:38.444 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out12333175762834823101.vcf
15:56:38.536 INFO  Funcotator - ------------------------------------------------------------
15:56:38.536 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:38.536 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:38.536 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:38.536 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:38.536 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:38 PM GMT
15:56:38.536 INFO  Funcotator - ------------------------------------------------------------
15:56:38.536 INFO  Funcotator - ------------------------------------------------------------
15:56:38.536 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:38.536 INFO  Funcotator - Picard Version: 3.4.0
15:56:38.536 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:38.536 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:38.536 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:38.536 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:38.536 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:38.536 INFO  Funcotator - Deflater: IntelDeflater
15:56:38.536 INFO  Funcotator - Inflater: IntelInflater
15:56:38.536 INFO  Funcotator - GCS max retries/reopens: 20
15:56:38.536 INFO  Funcotator - Requester pays: disabled
15:56:38.536 INFO  Funcotator - Initializing engine
15:56:38.538 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/Three_sample_somatic.vcf
15:56:38.538 INFO  Funcotator - Done initializing engine
15:56:38.538 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:38.538 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:38.538 INFO  Funcotator - Initializing data sources...
15:56:38.538 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:38.538 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:38.539 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
15:56:38.539 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
15:56:38.539 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
15:56:38.539 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:38.539 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
15:56:38.539 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:38.540 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
15:56:38.540 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
15:56:38.541 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
15:56:38.541 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:38.541 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
15:56:38.542 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
15:56:38.544 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
15:56:38.545 INFO  Funcotator - Initializing Funcotator Engine...
15:56:38.546 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:38.546 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.
15:56:38.546 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out7285565641746595111.maf
15:56:38.546 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:56:38.546 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:38 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:38.636 INFO  Funcotator - ------------------------------------------------------------
15:56:38.636 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:38.636 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:38.636 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:38.636 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:38.636 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:38 PM GMT
15:56:38.636 INFO  Funcotator - ------------------------------------------------------------
15:56:38.636 INFO  Funcotator - ------------------------------------------------------------
15:56:38.636 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:38.636 INFO  Funcotator - Picard Version: 3.4.0
15:56:38.636 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:38.636 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:38.636 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:38.636 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:38.636 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:38.636 INFO  Funcotator - Deflater: IntelDeflater
15:56:38.636 INFO  Funcotator - Inflater: IntelInflater
15:56:38.636 INFO  Funcotator - GCS max retries/reopens: 20
15:56:38.636 INFO  Funcotator - Requester pays: disabled
15:56:38.636 INFO  Funcotator - Initializing engine
15:56:38.637 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
15:56:38.650 INFO  Funcotator - Done initializing engine
15:56:38.650 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:38.650 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:38.650 INFO  Funcotator - Initializing data sources...
15:56:38.650 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:38.650 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:38.650 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
15:56:38.650 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
15:56:38.650 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
15:56:38.650 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:38.650 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
15:56:38.650 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:38.651 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
15:56:38.651 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
15:56:38.652 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
15:56:38.652 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:38.652 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
15:56:38.660 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
15:56:38.668 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
15:56:38.675 INFO  Funcotator - Initializing Funcotator Engine...
15:56:38.679 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:38.679 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out10478127780556469050.maf
15:56:38.680 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
15:56:38.680 INFO  ProgressMeter - Starting traversal
15:56:38.680 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:38.682 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)
15:56:38.683 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)
15:56:38.683 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:38.683 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:56:38.683 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:56:38.683 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:56:38.684 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199000 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+
15:56:38.688 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:38.688 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:56:38.688 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:56:38.688 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:56:38.688 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199001 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+
15:56:38.688 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)
15:56:38.689 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)
15:56:38.689 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:38.689 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:56:38.689 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:56:38.689 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:56:38.689 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199002 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+
15:56:38.689 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)
15:56:38.690 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)
15:56:38.690 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
15:56:38.690 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
15:56:38.690 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:56:38.690 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:56:38.690 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199003 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+
15:56:38.691 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:38.691 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:56:38.691 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:56:38.691 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:56:38.691 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199004 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+
15:56:38.692 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:38.692 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:56:38.692 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:56:38.692 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:56:38.692 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199005 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=
15:56:38.692 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)
15:56:38.693 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)
15:56:38.693 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:56:38.693 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:56:38.693 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:56:38.693 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:56:38.693 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199006 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=
15:56:38.693 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)
15:56:38.694 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)
15:56:38.694 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:38.694 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:56:38.694 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:56:38.694 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:56:38.694 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199007 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+
15:56:38.695 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:56:38.695 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:56:38.695 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:56:38.695 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:56:38.695 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199008 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+
15:56:38.695 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)
15:56:38.696 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)
15:56:38.696 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:56:38.696 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:56:38.696 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:56:38.696 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:56:38.696 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179199009 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=
15:56:38.696 INFO  ProgressMeter -             unmapped              0.0                    10          37500.0
15:56:38.696 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
15:56:38.696 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:56:38.697 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:38 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:56:38 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:38.889 INFO  Funcotator - ------------------------------------------------------------
15:56:38.889 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:38.889 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:38.889 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:38.889 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:38.889 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:38 PM GMT
15:56:38.889 INFO  Funcotator - ------------------------------------------------------------
15:56:38.889 INFO  Funcotator - ------------------------------------------------------------
15:56:38.890 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:38.890 INFO  Funcotator - Picard Version: 3.4.0
15:56:38.890 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:38.890 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:38.890 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:38.890 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:38.890 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:38.890 INFO  Funcotator - Deflater: IntelDeflater
15:56:38.890 INFO  Funcotator - Inflater: IntelInflater
15:56:38.890 INFO  Funcotator - GCS max retries/reopens: 20
15:56:38.890 INFO  Funcotator - Requester pays: disabled
15:56:38.890 INFO  Funcotator - Initializing engine
15:56:38.891 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
15:56:38.892 INFO  Funcotator - Done initializing engine
15:56:38.892 INFO  Funcotator - Validating sequence dictionaries...
15:56:38.893 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:38 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:38.981 INFO  Funcotator - ------------------------------------------------------------
15:56:38.981 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:38.981 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:38.981 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:38.981 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:38.981 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:38 PM GMT
15:56:38.981 INFO  Funcotator - ------------------------------------------------------------
15:56:38.981 INFO  Funcotator - ------------------------------------------------------------
15:56:38.981 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:38.981 INFO  Funcotator - Picard Version: 3.4.0
15:56:38.981 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:38.981 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:38.981 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:38.981 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:38.981 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:38.981 INFO  Funcotator - Deflater: IntelDeflater
15:56:38.981 INFO  Funcotator - Inflater: IntelInflater
15:56:38.981 INFO  Funcotator - GCS max retries/reopens: 20
15:56:38.981 INFO  Funcotator - Requester pays: disabled
15:56:38.981 INFO  Funcotator - Initializing engine
15:56:38.983 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
15:56:38.984 INFO  Funcotator - Done initializing engine
15:56:38.984 INFO  Funcotator - Validating sequence dictionaries...
15:56:38.984 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:38.984 INFO  Funcotator - Initializing data sources...
15:56:38.984 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:38.984 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:38.985 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
15:56:38.985 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
15:56:38.985 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
15:56:38.985 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
15:56:38.985 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
15:56:38.986 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
15:56:38.986 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:38.986 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:38.986 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
15:56:38.986 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
15:56:38.986 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
15:56:38.987 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
15:56:38.987 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:38.987 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
15:56:38.987 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
15:56:38.987 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:38.987 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
15:56:38.987 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
15:56:39.006 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
15:56:39.007 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
15:56:39.051 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
15:56:39.052 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
15:56:39.587 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:39.587 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:39.588 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:39.590 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:39.593 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:39.595 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:39.595 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:39.596 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:39.623 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
15:56:39.623 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
WARNING	2025-05-27 15:56:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:39.624 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
15:56:39.662 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
15:56:39.662 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
15:56:39.663 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
15:56:39.670 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:39.671 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
15:56:39.671 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:39.671 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:39.672 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
15:56:39.757 INFO  Funcotator - Initializing Funcotator Engine...
15:56:39.758 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:56:39.758 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.
15:56:39.758 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator11174939043986453876.vcf
15:56:39.760 INFO  ProgressMeter - Starting traversal
15:56:39.760 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:41.712 INFO  ProgressMeter -             unmapped              0.0                   198           6086.1
15:56:41.712 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:56:41.712 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:56:41.721 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:41 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3261071360
15:56:41.822 INFO  Funcotator - ------------------------------------------------------------
15:56:41.822 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:41.822 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:41.822 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:41.822 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:41.822 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:41 PM GMT
15:56:41.822 INFO  Funcotator - ------------------------------------------------------------
15:56:41.822 INFO  Funcotator - ------------------------------------------------------------
15:56:41.822 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:41.822 INFO  Funcotator - Picard Version: 3.4.0
15:56:41.822 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:41.822 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:41.822 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:41.822 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:41.822 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:41.822 INFO  Funcotator - Deflater: IntelDeflater
15:56:41.822 INFO  Funcotator - Inflater: IntelInflater
15:56:41.822 INFO  Funcotator - GCS max retries/reopens: 20
15:56:41.822 INFO  Funcotator - Requester pays: disabled
15:56:41.822 INFO  Funcotator - Initializing engine
15:56:41.824 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
15:56:41.825 INFO  Funcotator - Done initializing engine
15:56:41.825 INFO  Funcotator - Validating sequence dictionaries...
15:56:41.825 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:41.825 INFO  Funcotator - Initializing data sources...
15:56:41.825 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:41.825 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:41.826 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
15:56:41.826 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
15:56:41.826 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
15:56:41.826 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
15:56:41.826 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
15:56:41.826 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
15:56:41.826 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:41.827 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:41.827 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
15:56:41.827 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
15:56:41.827 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
15:56:41.827 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
15:56:41.827 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:41.828 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
15:56:41.828 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
15:56:41.828 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:41.828 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
15:56:41.828 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
15:56:41.847 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:56:41.847 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
15:56:41.892 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
15:56:41.893 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
15:56:42.466 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:42.466 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:42.467 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:42.469 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:42.471 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:42.473 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:42.474 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:42.474 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:42.502 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
15:56:42.502 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	2025-05-27 15:56:42	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:42.502 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
15:56:42.541 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
15:56:42.541 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
15:56:42.541 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
15:56:42.549 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:42.549 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
15:56:42.549 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:42.550 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:42.550 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
15:56:42.635 INFO  Funcotator - Initializing Funcotator Engine...
15:56:42.635 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:56:42.635 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.
15:56:42.635 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator5160995957284628914.maf
15:56:42.636 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
15:56:42.636 INFO  ProgressMeter - Starting traversal
15:56:42.636 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:44.532 INFO  ProgressMeter -             unmapped              0.0                   198           6265.8
15:56:44.532 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:56:44.532 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:56:44.533 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:44 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3261071360
15:56:44.625 INFO  Funcotator - ------------------------------------------------------------
15:56:44.625 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:44.625 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:44.625 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:44.625 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:44.625 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:44 PM GMT
15:56:44.625 INFO  Funcotator - ------------------------------------------------------------
15:56:44.625 INFO  Funcotator - ------------------------------------------------------------
15:56:44.625 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:44.625 INFO  Funcotator - Picard Version: 3.4.0
15:56:44.625 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:44.625 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:44.625 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:44.625 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:44.625 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:44.625 INFO  Funcotator - Deflater: IntelDeflater
15:56:44.625 INFO  Funcotator - Inflater: IntelInflater
15:56:44.625 INFO  Funcotator - GCS max retries/reopens: 20
15:56:44.625 INFO  Funcotator - Requester pays: disabled
15:56:44.625 INFO  Funcotator - Initializing engine
15:56:44.653 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/badDataOneAlleleDepthValue_hg38.vcf
15:56:44.674 INFO  Funcotator - Done initializing engine
15:56:44.674 INFO  Funcotator - Validating sequence dictionaries...
15:56:44.681 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:44.681 INFO  Funcotator - Initializing data sources...
15:56:44.681 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:44.681 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:44.681 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
15:56:44.681 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
15:56:44.682 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:56:44.682 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
15:56:44.682 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
15:56:44.682 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
15:56:44.682 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
15:56:44.682 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
15:56:44.682 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
15:56:44.683 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
15:56:44.683 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
15:56:44.683 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
15:56:44.683 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
15:56:44.683 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:44.683 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
15:56:44.683 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
15:56:44.702 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
15:56:44.703 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
15:56:44.748 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
15:56:44.749 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
15:56:45.306 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
15:56:45.306 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:45.307 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:56:45.308 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
15:56:45.310 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:56:45.311 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
15:56:45.377 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
15:56:45.377 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
15:56:45.378 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
15:56:45.385 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
15:56:45.385 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:45.386 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
15:56:45.386 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
15:56:45.387 INFO  Funcotator - Initializing Funcotator Engine...
15:56:45.391 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:45.391 INFO  Funcotator - Creating a MAF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator13878133928760417382.vcf
15:56:45.392 INFO  ProgressMeter - Starting traversal
15:56:45.392 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:45.396 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:56:45.400 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:45 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360
15:56:45.491 INFO  Funcotator - ------------------------------------------------------------
15:56:45.491 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:45.491 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:45.491 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:45.491 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:45.491 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:45 PM GMT
15:56:45.491 INFO  Funcotator - ------------------------------------------------------------
15:56:45.491 INFO  Funcotator - ------------------------------------------------------------
15:56:45.491 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:45.491 INFO  Funcotator - Picard Version: 3.4.0
15:56:45.491 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:45.491 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:45.491 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:45.491 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:45.491 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:45.491 INFO  Funcotator - Deflater: IntelDeflater
15:56:45.491 INFO  Funcotator - Inflater: IntelInflater
15:56:45.491 INFO  Funcotator - GCS max retries/reopens: 20
15:56:45.491 INFO  Funcotator - Requester pays: disabled
15:56:45.491 INFO  Funcotator - Initializing engine
15:56:45.494 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/vcfBugRepro.vcf
15:56:45.494 INFO  Funcotator - Done initializing engine
15:56:45.494 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:45.494 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:45.494 INFO  Funcotator - Initializing data sources...
15:56:45.494 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/
15:56:45.494 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:45.494 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
15:56:45.494 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
15:56:45.494 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
15:56:45.495 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:45.495 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
15:56:45.495 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
15:56:45.495 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
15:56:45.495 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
15:56:45.496 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
15:56:45.496 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
15:56:45.496 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:45.497 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
15:56:45.497 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
15:56:45.497 INFO  Funcotator - Initializing Funcotator Engine...
15:56:45.497 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:45.497 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.
15:56:45.497 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:45.497 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing6098547614619516142.vcf
15:56:45.498 INFO  ProgressMeter - Starting traversal
15:56:45.498 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:45.502 INFO  ProgressMeter -             unmapped              0.0                     1          15000.0
15:56:45.502 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:56:45.503 INFO  VcfFuncotationFactory - dbSnp fake cache hits/total: 0/1
15:56:45.505 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:45 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:45.505 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing6098547614619516142.vcf
15:56:45.595 INFO  Funcotator - ------------------------------------------------------------
15:56:45.595 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:45.595 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:45.595 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:45.595 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:45.595 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:45 PM GMT
15:56:45.595 INFO  Funcotator - ------------------------------------------------------------
15:56:45.595 INFO  Funcotator - ------------------------------------------------------------
15:56:45.595 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:45.595 INFO  Funcotator - Picard Version: 3.4.0
15:56:45.595 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:45.595 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:45.595 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:45.595 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:45.595 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:45.595 INFO  Funcotator - Deflater: IntelDeflater
15:56:45.595 INFO  Funcotator - Inflater: IntelInflater
15:56:45.595 INFO  Funcotator - GCS max retries/reopens: 20
15:56:45.595 INFO  Funcotator - Requester pays: disabled
15:56:45.595 INFO  Funcotator - Initializing engine
15:56:45.596 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:56:45.597 INFO  Funcotator - Done initializing engine
15:56:45.597 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:45.597 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:45.597 INFO  Funcotator - Initializing data sources...
15:56:45.597 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:45.597 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:45.597 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
15:56:45.597 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
15:56:45.597 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
15:56:45.597 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:45.597 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
15:56:45.598 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:45.598 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
15:56:45.598 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
15:56:45.599 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
15:56:45.599 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:45.599 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
15:56:45.600 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
15:56:45.601 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
15:56:45.602 INFO  Funcotator - Initializing Funcotator Engine...
15:56:45.602 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:45.602 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.
15:56:45.602 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6922594230676286545.maf
15:56:45.602 INFO  ProgressMeter - Starting traversal
15:56:45.602 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:45.605 WARN  MafOutputRenderer - 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=
15:56:45.606 WARN  MafOutputRenderer - 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=
15:56:45.606 WARN  MafOutputRenderer - 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=
15:56:45.607 WARN  MafOutputRenderer - 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=
15:56:45.607 WARN  MafOutputRenderer - 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=
15:56:45.608 WARN  MafOutputRenderer - 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=
15:56:45.608 WARN  MafOutputRenderer - 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=
15:56:45.609 WARN  MafOutputRenderer - 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=
15:56:45.609 WARN  MafOutputRenderer - 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=
15:56:45.609 WARN  MafOutputRenderer - 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=
15:56:45.610 WARN  MafOutputRenderer - 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=
15:56:45.610 WARN  MafOutputRenderer - 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=
15:56:45.610 WARN  MafOutputRenderer - 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=
15:56:45.611 WARN  MafOutputRenderer - 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=
15:56:45.611 WARN  MafOutputRenderer - 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=
15:56:45.611 WARN  MafOutputRenderer - 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=
15:56:45.612 WARN  MafOutputRenderer - 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=
15:56:45.612 WARN  MafOutputRenderer - 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=
15:56:45.612 WARN  MafOutputRenderer - 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=
15:56:45.613 WARN  MafOutputRenderer - 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=
15:56:45.613 WARN  MafOutputRenderer - 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=
15:56:45.613 INFO  ProgressMeter -             unmapped              0.0                    21         114545.5
15:56:45.613 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:56:45.613 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:56:45.613 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:45 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:45.616 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
15:56:45.618 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:56:45.711 INFO  Funcotator - ------------------------------------------------------------
15:56:45.711 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:45.711 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:45.711 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:45.711 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:45.711 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:45 PM GMT
15:56:45.711 INFO  Funcotator - ------------------------------------------------------------
15:56:45.711 INFO  Funcotator - ------------------------------------------------------------
15:56:45.711 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:45.711 INFO  Funcotator - Picard Version: 3.4.0
15:56:45.711 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:45.711 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:45.711 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:45.711 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:45.711 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:45.711 INFO  Funcotator - Deflater: IntelDeflater
15:56:45.711 INFO  Funcotator - Inflater: IntelInflater
15:56:45.711 INFO  Funcotator - GCS max retries/reopens: 20
15:56:45.711 INFO  Funcotator - Requester pays: disabled
15:56:45.711 INFO  Funcotator - Initializing engine
15:56:45.712 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:56:45.713 INFO  Funcotator - Done initializing engine
15:56:45.713 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:45.713 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:45.714 INFO  Funcotator - Initializing data sources...
15:56:45.714 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:45.714 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:45.714 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
15:56:45.714 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
15:56:45.714 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
15:56:45.714 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:45.714 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
15:56:45.714 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:45.715 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
15:56:45.715 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
15:56:45.715 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
15:56:45.715 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:45.716 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
15:56:45.716 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
15:56:45.718 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
15:56:45.718 INFO  Funcotator - Initializing Funcotator Engine...
15:56:45.718 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:45.718 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.
15:56:45.718 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out7294453942714926345.vcf
15:56:45.722 INFO  ProgressMeter - Starting traversal
15:56:45.722 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:45.731 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
15:56:45.731 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:56:45.731 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:56:45.733 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:45 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:45.734 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out7294453942714926345.vcf
15:56:45.825 INFO  Funcotator - ------------------------------------------------------------
15:56:45.825 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:45.825 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:45.825 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:45.825 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:45.825 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:45 PM GMT
15:56:45.825 INFO  Funcotator - ------------------------------------------------------------
15:56:45.825 INFO  Funcotator - ------------------------------------------------------------
15:56:45.825 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:45.825 INFO  Funcotator - Picard Version: 3.4.0
15:56:45.825 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:45.825 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:45.825 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:45.825 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:45.825 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:45.825 INFO  Funcotator - Deflater: IntelDeflater
15:56:45.825 INFO  Funcotator - Inflater: IntelInflater
15:56:45.825 INFO  Funcotator - GCS max retries/reopens: 20
15:56:45.825 INFO  Funcotator - Requester pays: disabled
15:56:45.825 INFO  Funcotator - Initializing engine
15:56:45.826 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
15:56:45.826 INFO  Funcotator - Done initializing engine
15:56:45.826 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:45.826 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:45.826 INFO  Funcotator - Initializing data sources...
15:56:45.826 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:45.826 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:45.827 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
15:56:45.827 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
15:56:45.827 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
15:56:45.827 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:45.827 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
15:56:45.827 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:45.828 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
15:56:45.828 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
15:56:45.828 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
15:56:45.828 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:45.829 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
15:56:45.829 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
15:56:45.831 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
15:56:45.831 INFO  Funcotator - Initializing Funcotator Engine...
15:56:45.831 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:45.831 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.
15:56:45.831 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:45.831 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out1896091036755820864.vcf
15:56:45.832 INFO  ProgressMeter - Starting traversal
15:56:45.832 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:45.836 INFO  ProgressMeter -             unmapped              0.0                     5          75000.0
15:56:45.836 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
15:56:45.836 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:56:45.839 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:45 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:45.839 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out1896091036755820864.vcf
15:56:45.930 INFO  Funcotator - ------------------------------------------------------------
15:56:45.930 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:45.930 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:45.930 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:45.930 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:45.930 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:45 PM GMT
15:56:45.930 INFO  Funcotator - ------------------------------------------------------------
15:56:45.930 INFO  Funcotator - ------------------------------------------------------------
15:56:45.930 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:45.930 INFO  Funcotator - Picard Version: 3.4.0
15:56:45.930 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:45.930 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:45.930 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:45.930 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:45.930 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:45.930 INFO  Funcotator - Deflater: IntelDeflater
15:56:45.930 INFO  Funcotator - Inflater: IntelInflater
15:56:45.930 INFO  Funcotator - GCS max retries/reopens: 20
15:56:45.930 INFO  Funcotator - Requester pays: disabled
15:56:45.930 INFO  Funcotator - Initializing engine
15:56:45.932 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
15:56:45.932 INFO  Funcotator - Done initializing engine
15:56:45.932 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:45.932 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:45.932 INFO  Funcotator - Initializing data sources...
15:56:45.932 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:45.932 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:45.933 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
15:56:45.933 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
15:56:45.933 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:56:45.933 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:45.933 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
15:56:45.933 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:45.934 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
15:56:45.934 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
15:56:45.934 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:56:45.935 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:45.935 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:56:45.936 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
15:56:45.938 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
15:56:45.939 INFO  Funcotator - Initializing Funcotator Engine...
15:56:45.939 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:45.939 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.
15:56:45.939 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:45.939 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out2595406455953352165.vcf
15:56:45.940 INFO  ProgressMeter - Starting traversal
15:56:45.940 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:45.953 INFO  ProgressMeter -             unmapped              0.0                    15          69230.8
15:56:45.953 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
15:56:45.953 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
15:56:45.956 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:45 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:46.048 INFO  Funcotator - ------------------------------------------------------------
15:56:46.048 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:46.048 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:46.048 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:46.048 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:46.048 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:46 PM GMT
15:56:46.048 INFO  Funcotator - ------------------------------------------------------------
15:56:46.048 INFO  Funcotator - ------------------------------------------------------------
15:56:46.048 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:46.048 INFO  Funcotator - Picard Version: 3.4.0
15:56:46.048 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:46.048 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:46.048 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:46.048 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:46.048 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:46.048 INFO  Funcotator - Deflater: IntelDeflater
15:56:46.048 INFO  Funcotator - Inflater: IntelInflater
15:56:46.048 INFO  Funcotator - GCS max retries/reopens: 20
15:56:46.048 INFO  Funcotator - Requester pays: disabled
15:56:46.048 INFO  Funcotator - Initializing engine
15:56:46.050 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
15:56:46.050 INFO  Funcotator - Done initializing engine
15:56:46.050 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:46.050 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:46.050 INFO  Funcotator - Initializing data sources...
15:56:46.050 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:46.050 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:46.051 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
15:56:46.051 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
15:56:46.051 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
15:56:46.051 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:46.051 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
15:56:46.051 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:46.052 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
15:56:46.052 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
15:56:46.052 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
15:56:46.052 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:46.053 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
15:56:46.054 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
15:56:46.055 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
15:56:46.056 INFO  Funcotator - Initializing Funcotator Engine...
15:56:46.056 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:46.056 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.
15:56:46.056 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:46.056 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out13471536416627019172.maf
15:56:46.056 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
15:56:46.057 INFO  ProgressMeter - Starting traversal
15:56:46.057 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:46.059 WARN  MafOutputRenderer - 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=
15:56:46.059 WARN  MafOutputRenderer - 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=
15:56:46.061 WARN  MafOutputRenderer - 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=
15:56:46.061 WARN  MafOutputRenderer - 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=
15:56:46.061 WARN  MafOutputRenderer - 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=
15:56:46.062 WARN  MafOutputRenderer - 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=
15:56:46.062 WARN  MafOutputRenderer - 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=
15:56:46.063 WARN  MafOutputRenderer - 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=
15:56:46.063 WARN  MafOutputRenderer - 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=
15:56:46.063 WARN  MafOutputRenderer - 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=
15:56:46.064 WARN  MafOutputRenderer - 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=
15:56:46.064 WARN  MafOutputRenderer - 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=
15:56:46.064 WARN  MafOutputRenderer - 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=
15:56:46.065 WARN  MafOutputRenderer - 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=
15:56:46.065 WARN  MafOutputRenderer - 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=
15:56:46.065 INFO  ProgressMeter -             unmapped              0.0                    15         112500.0
15:56:46.065 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
15:56:46.065 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
15:56:46.065 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:46 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:46.066 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out2595406455953352165.vcf
15:56:46.159 INFO  Funcotator - ------------------------------------------------------------
15:56:46.159 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:46.159 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:46.159 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:46.159 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:46.159 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:46 PM GMT
15:56:46.159 INFO  Funcotator - ------------------------------------------------------------
15:56:46.159 INFO  Funcotator - ------------------------------------------------------------
15:56:46.160 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:46.160 INFO  Funcotator - Picard Version: 3.4.0
15:56:46.160 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:46.160 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:46.160 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:46.160 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:46.160 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:46.160 INFO  Funcotator - Deflater: IntelDeflater
15:56:46.160 INFO  Funcotator - Inflater: IntelInflater
15:56:46.160 INFO  Funcotator - GCS max retries/reopens: 20
15:56:46.160 INFO  Funcotator - Requester pays: disabled
15:56:46.160 INFO  Funcotator - Initializing engine
15:56:46.161 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
15:56:46.161 INFO  Funcotator - Done initializing engine
15:56:46.161 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:46.161 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:46.161 INFO  Funcotator - Initializing data sources...
15:56:46.161 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:46.161 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:46.161 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
15:56:46.161 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
15:56:46.162 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
15:56:46.162 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:46.162 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
15:56:46.162 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:46.162 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
15:56:46.163 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
15:56:46.163 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
15:56:46.163 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:46.164 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
15:56:46.164 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
15:56:46.165 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
15:56:46.166 INFO  Funcotator - Initializing Funcotator Engine...
15:56:46.166 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:46.166 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.
15:56:46.166 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:46.166 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6297951519957215075.vcf
15:56:46.167 INFO  ProgressMeter - Starting traversal
15:56:46.167 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:46.198 INFO  ProgressMeter -             unmapped              0.0                    57         114000.0
15:56:46.198 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:56:46.198 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:56:46.200 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:46 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:46.293 INFO  Funcotator - ------------------------------------------------------------
15:56:46.293 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:46.293 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:46.293 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:46.293 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:46.293 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:46 PM GMT
15:56:46.293 INFO  Funcotator - ------------------------------------------------------------
15:56:46.293 INFO  Funcotator - ------------------------------------------------------------
15:56:46.293 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:46.293 INFO  Funcotator - Picard Version: 3.4.0
15:56:46.293 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:46.293 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:46.293 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:46.293 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:46.293 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:46.293 INFO  Funcotator - Deflater: IntelDeflater
15:56:46.293 INFO  Funcotator - Inflater: IntelInflater
15:56:46.293 INFO  Funcotator - GCS max retries/reopens: 20
15:56:46.293 INFO  Funcotator - Requester pays: disabled
15:56:46.293 INFO  Funcotator - Initializing engine
15:56:46.294 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
15:56:46.295 INFO  Funcotator - Done initializing engine
15:56:46.295 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:46.295 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:46.295 INFO  Funcotator - Initializing data sources...
15:56:46.295 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:56:46.295 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:46.295 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
15:56:46.295 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
15:56:46.295 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:56:46.295 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:46.295 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
15:56:46.295 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:46.296 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
15:56:46.296 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
15:56:46.296 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
15:56:46.296 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:56:46.297 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:56:46.298 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:56:46.299 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:56:46.300 INFO  Funcotator - Initializing Funcotator Engine...
15:56:46.300 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:56:46.300 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.
15:56:46.300 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:46.300 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out3575674026574098709.maf
15:56:46.300 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
15:56:46.300 INFO  ProgressMeter - Starting traversal
15:56:46.300 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:56:46.303 WARN  MafOutputRenderer - 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=
15:56:46.303 WARN  MafOutputRenderer - 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=
15:56:46.303 WARN  MafOutputRenderer - 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=
15:56:46.304 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
15:56:46.305 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCG] attr={} GT=[] filters=
15:56:46.305 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGA] attr={} GT=[] filters=
15:56:46.306 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
15:56:46.307 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948154 Q40.00 of type=INDEL alleles=[G*, GGAATT] attr={} GT=[] filters=
15:56:46.307 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
15:56:46.307 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
15:56:46.308 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948157 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
15:56:46.308 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948158 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
15:56:46.308 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, ATGA] attr={} GT=[] filters=
15:56:46.310 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916937-178916940 Q40.00 of type=INDEL alleles=[TGAA*, T] attr={} GT=[] filters=
15:56:46.310 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948162 Q40.00 of type=INDEL alleles=[TGAG*, T] attr={} GT=[] filters=
15:56:46.310 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948161 Q40.00 of type=INDEL alleles=[TGA*, T] attr={} GT=[] filters=
15:56:46.311 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948158 Q40.00 of type=INDEL alleles=[AGAATT*, A] attr={} GT=[] filters=
15:56:46.312 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948153-178948157 Q40.00 of type=INDEL alleles=[AGAAT*, A] attr={} GT=[] filters=
15:56:46.312 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159-178948164 Q40.00 of type=INDEL alleles=[TGAGAG*, T] attr={} GT=[] filters=
15:56:46.312 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165-178948168 Q40.00 of type=INDEL alleles=[GTGA*, G] attr={} GT=[] filters=
15:56:46.313 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
15:56:46.314 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATAT] attr={} GT=[] filters=
15:56:46.315 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTAT] attr={} GT=[] filters=
15:56:46.316 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
15:56:46.316 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ACTTGAAGAA] attr={} GT=[] filters=
15:56:46.317 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
15:56:46.318 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATA] attr={} GT=[] filters=
15:56:46.319 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTA] attr={} GT=[] filters=
15:56:46.319 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
15:56:46.320 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
15:56:46.320 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
15:56:46.321 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
15:56:46.322 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
15:56:46.322 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
15:56:46.322 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATATT] attr={} GT=[] filters=
15:56:46.324 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
15:56:46.324 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
15:56:46.325 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916621 Q40.00 of type=INDEL alleles=[CTCC*, C] attr={} GT=[] filters=
15:56:46.326 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916622 Q40.00 of type=INDEL alleles=[TCCA*, T] attr={} GT=[] filters=
15:56:46.326 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916623 Q40.00 of type=INDEL alleles=[CCAC*, C] attr={} GT=[] filters=
15:56:46.326 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916624 Q40.00 of type=INDEL alleles=[CACG*, C] attr={} GT=[] filters=
15:56:46.328 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916620 Q40.00 of type=INDEL alleles=[CTC*, C] attr={} GT=[] filters=
15:56:46.328 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916621 Q40.00 of type=INDEL alleles=[TCC*, T] attr={} GT=[] filters=
15:56:46.328 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916622 Q40.00 of type=INDEL alleles=[CCA*, C] attr={} GT=[] filters=
15:56:46.329 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916623 Q40.00 of type=INDEL alleles=[CAC*, C] attr={} GT=[] filters=
15:56:46.330 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916619 Q40.00 of type=INDEL alleles=[CT*, C] attr={} GT=[] filters=
15:56:46.330 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916620 Q40.00 of type=INDEL alleles=[TC*, T] attr={} GT=[] filters=
15:56:46.331 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
15:56:46.331 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
15:56:46.332 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916622 Q40.00 of type=INDEL alleles=[CTCCA*, C] attr={} GT=[] filters=
15:56:46.333 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916623 Q40.00 of type=INDEL alleles=[TCCAC*, T] attr={} GT=[] filters=
15:56:46.333 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916624 Q40.00 of type=INDEL alleles=[CCACG*, C] attr={} GT=[] filters=
15:56:46.333 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916625 Q40.00 of type=INDEL alleles=[CACGA*, C] attr={} GT=[] filters=
15:56:46.335 WARN  MafOutputRenderer - 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=
15:56:46.335 WARN  MafOutputRenderer - 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=
15:56:46.335 WARN  MafOutputRenderer - 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=
15:56:46.336 WARN  MafOutputRenderer - 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=
15:56:46.336 INFO  ProgressMeter -             unmapped              0.0                    57          95000.0
15:56:46.336 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:56:46.336 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:56:46.336 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:56:46 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:56:46.337 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out6297951519957215075.vcf
15:56:46.439 INFO  Funcotator - ------------------------------------------------------------
15:56:46.439 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:56:46.439 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:46.439 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:56:46.439 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:46.439 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:56:46 PM GMT
15:56:46.439 INFO  Funcotator - ------------------------------------------------------------
15:56:46.439 INFO  Funcotator - ------------------------------------------------------------
15:56:46.439 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:46.439 INFO  Funcotator - Picard Version: 3.4.0
15:56:46.439 INFO  Funcotator - Built for Spark Version: 3.5.0
15:56:46.439 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:46.439 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:46.439 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:46.439 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:46.439 INFO  Funcotator - Deflater: IntelDeflater
15:56:46.439 INFO  Funcotator - Inflater: IntelInflater
15:56:46.439 INFO  Funcotator - GCS max retries/reopens: 20
15:56:46.439 INFO  Funcotator - Requester pays: disabled
15:56:46.439 INFO  Funcotator - Initializing engine
15:56:46.440 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
15:56:46.441 INFO  Funcotator - Done initializing engine
15:56:46.441 INFO  Funcotator - Skipping sequence dictionary validation.
15:56:46.441 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:56:46.441 INFO  Funcotator - Initializing data sources...
15:56:46.441 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:56:46.441 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:56:46.441 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
15:56:46.442 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
15:56:46.442 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
15:56:46.442 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
15:56:46.442 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
15:56:46.442 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
15:56:46.442 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:46.443 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:46.443 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
15:56:46.443 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
15:56:46.443 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
15:56:46.443 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
15:56:46.443 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:46.444 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
15:56:46.444 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
15:56:46.444 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:56:46.444 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
15:56:46.444 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
15:56:46.463 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
15:56:46.464 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
15:56:46.509 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
15:56:46.509 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
15:56:47.056 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:47.056 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:56:47.057 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:47.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:47.062 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:56:47.064 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:56:47.064 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:47.064 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:56:47.092 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:56:47.092 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:56:47	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:56:47.092 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
15:56:47.131 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
15:56:47.131 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
15:56:47.131 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
15:56:47.197 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:56:47.197 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
15:56:47.197 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:56:47.198 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:56:47.198 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
15:56:47.283 INFO  Funcotator - Initializing Funcotator Engine...
15:56:47.283 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:56:47.283 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:56:47.283 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4345433332885877486.vcf
15:56:47.284 INFO  ProgressMeter - Starting traversal
15:56:47.284 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:57:02.008 INFO  ProgressMeter -        chr19:9077594              0.2                  2000           8150.0
15:57:02.438 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)
15:57:02.439 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)
15:57:03.132 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7787.7
15:57:03.132 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
15:57:03.132 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
15:57:03.134 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:57:03 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.28 minutes.
Runtime.totalMemory()=3261071360
15:57:03.238 INFO  Funcotator - ------------------------------------------------------------
15:57:03.238 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:57:03.238 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:57:03.239 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:57:03.239 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:57:03.239 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:57:03 PM GMT
15:57:03.239 INFO  Funcotator - ------------------------------------------------------------
15:57:03.239 INFO  Funcotator - ------------------------------------------------------------
15:57:03.239 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:57:03.239 INFO  Funcotator - Picard Version: 3.4.0
15:57:03.239 INFO  Funcotator - Built for Spark Version: 3.5.0
15:57:03.239 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:57:03.239 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:57:03.239 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:57:03.239 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:57:03.239 INFO  Funcotator - Deflater: IntelDeflater
15:57:03.239 INFO  Funcotator - Inflater: IntelInflater
15:57:03.239 INFO  Funcotator - GCS max retries/reopens: 20
15:57:03.239 INFO  Funcotator - Requester pays: disabled
15:57:03.239 INFO  Funcotator - Initializing engine
15:57:03.240 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
15:57:03.240 INFO  Funcotator - Done initializing engine
15:57:03.240 INFO  Funcotator - Skipping sequence dictionary validation.
15:57:03.240 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:57:03.240 INFO  Funcotator - Initializing data sources...
15:57:03.240 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:57:03.240 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:57:03.241 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
15:57:03.241 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
15:57:03.241 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
15:57:03.241 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
15:57:03.241 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
15:57:03.241 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
15:57:03.242 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:57:03.242 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
15:57:03.242 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
15:57:03.242 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
15:57:03.242 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
15:57:03.242 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
15:57:03.243 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:57:03.243 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
15:57:03.243 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
15:57:03.243 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:57:03.243 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
15:57:03.243 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
15:57:03.262 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
15:57:03.263 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
15:57:03.308 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
15:57:03.308 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
15:57:03.882 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:57:03.882 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:57:03.883 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:57:03.885 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:57:03.888 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:57:03.890 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:57:03.890 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:57:03.890 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:57:03.918 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:57:03.918 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:57:03	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:57:03.918 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
15:57:03.957 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:57:03.957 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:57:03.957 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
15:57:03.965 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:57:03.965 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:57:03.965 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:57:03.966 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:57:03.966 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
15:57:04.053 INFO  Funcotator - Initializing Funcotator Engine...
15:57:04.053 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:57:04.053 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:57:04.053 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out15672476789645065806.maf
15:57:04.053 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
15:57:04.054 INFO  ProgressMeter - Starting traversal
15:57:04.054 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:57:18.615 INFO  ProgressMeter -        chr19:9077594              0.2                  2000           8241.2
15:57:19.066 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)
15:57:19.067 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)
15:57:19.765 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7855.6
15:57:19.765 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
15:57:19.765 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
15:57:19.766 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:57:19 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.28 minutes.
Runtime.totalMemory()=3261071360
15:57:19.767 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4345433332885877486.vcf
15:57:20.176 INFO  Funcotator - ------------------------------------------------------------
15:57:20.176 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:57:20.176 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:57:20.176 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:57:20.176 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:57:20.176 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:57:20 PM GMT
15:57:20.176 INFO  Funcotator - ------------------------------------------------------------
15:57:20.176 INFO  Funcotator - ------------------------------------------------------------
15:57:20.176 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:57:20.176 INFO  Funcotator - Picard Version: 3.4.0
15:57:20.176 INFO  Funcotator - Built for Spark Version: 3.5.0
15:57:20.176 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:57:20.176 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:57:20.176 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:57:20.176 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:57:20.176 INFO  Funcotator - Deflater: IntelDeflater
15:57:20.176 INFO  Funcotator - Inflater: IntelInflater
15:57:20.176 INFO  Funcotator - GCS max retries/reopens: 20
15:57:20.177 INFO  Funcotator - Requester pays: disabled
15:57:20.177 INFO  Funcotator - Initializing engine
15:57:20.177 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:57:20.194 INFO  Funcotator - Done initializing engine
15:57:20.194 INFO  Funcotator - Skipping sequence dictionary validation.
15:57:20.194 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:57:20.194 INFO  Funcotator - Initializing data sources...
15:57:20.194 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:57:20.194 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:57:20.195 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
15:57:20.195 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
15:57:20.195 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
15:57:20.195 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:57:20.195 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
15:57:20.195 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:57:20.195 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
15:57:20.196 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
15:57:20.196 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
15:57:20.196 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:57:20.197 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
15:57:20.204 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
15:57:20.213 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
15:57:20.221 INFO  Funcotator - Initializing Funcotator Engine...
15:57:20.227 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:57:20.227 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13348572936586684743.vcf
15:57:20.239 INFO  ProgressMeter - Starting traversal
15:57:20.239 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:57:20.266 INFO  ProgressMeter -             unmapped              0.0                   100         222222.2
15:57:20.266 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:57:20.266 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:57:20.271 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:57:20 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:57:20.362 INFO  Funcotator - ------------------------------------------------------------
15:57:20.362 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:57:20.362 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:57:20.362 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:57:20.362 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:57:20.362 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:57:20 PM GMT
15:57:20.362 INFO  Funcotator - ------------------------------------------------------------
15:57:20.362 INFO  Funcotator - ------------------------------------------------------------
15:57:20.362 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:57:20.362 INFO  Funcotator - Picard Version: 3.4.0
15:57:20.362 INFO  Funcotator - Built for Spark Version: 3.5.0
15:57:20.362 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:57:20.362 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:57:20.362 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:57:20.362 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:57:20.362 INFO  Funcotator - Deflater: IntelDeflater
15:57:20.362 INFO  Funcotator - Inflater: IntelInflater
15:57:20.362 INFO  Funcotator - GCS max retries/reopens: 20
15:57:20.362 INFO  Funcotator - Requester pays: disabled
15:57:20.362 INFO  Funcotator - Initializing engine
15:57:20.363 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:57:20.380 INFO  Funcotator - Done initializing engine
15:57:20.380 INFO  Funcotator - Skipping sequence dictionary validation.
15:57:20.380 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:57:20.380 INFO  Funcotator - Initializing data sources...
15:57:20.380 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:57:20.380 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:57:20.380 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
15:57:20.380 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
15:57:20.381 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
15:57:20.381 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:57:20.381 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
15:57:20.381 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:57:20.381 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
15:57:20.382 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
15:57:20.382 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
15:57:20.382 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:57:20.383 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
15:57:20.390 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
15:57:20.398 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
15:57:20.406 INFO  Funcotator - Initializing Funcotator Engine...
15:57:20.413 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:57:20.413 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out12945963282299209030.maf
15:57:20.413 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
15:57:20.414 INFO  ProgressMeter - Starting traversal
15:57:20.414 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:57:20.416 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179126640-179126641 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=
15:57:20.421 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 @ 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=
15:57:20.421 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 @ 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+
15:57:20.421 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 @ 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+
15:57:20.421 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 @ 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+
15:57:20.422 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 @ 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+
15:57:20.422 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 @ 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=
15:57:20.423 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 @ 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=
15:57:20.423 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 @ 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=
15:57:20.423 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 @ 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=
15:57:20.423 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 @ 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=
15:57:20.423 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 @ 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=
15:57:20.424 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:57:20.424 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:57:20.424 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:57:20.425 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:57:20.425 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:57:20.425 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:57:20.426 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:57:20.426 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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+
15:57:20.426 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
15:57:20.427 WARN  MafOutputRenderer - 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=
15:57:20.427 WARN  MafOutputRenderer - 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=
15:57:20.427 WARN  MafOutputRenderer - 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=
15:57:20.427 WARN  MafOutputRenderer - 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=
15:57:20.428 WARN  MafOutputRenderer - 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=
15:57:20.428 WARN  MafOutputRenderer - 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=
15:57:20.428 WARN  MafOutputRenderer - 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=
15:57:20.428 WARN  MafOutputRenderer - 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
15:57:20.428 WARN  MafOutputRenderer - 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=
15:57:20.429 WARN  MafOutputRenderer - 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=
15:57:20.429 WARN  MafOutputRenderer - 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=
15:57:20.429 WARN  MafOutputRenderer - 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=
15:57:20.429 WARN  MafOutputRenderer - 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=
15:57:20.430 WARN  MafOutputRenderer - 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=
15:57:20.430 WARN  MafOutputRenderer - 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=
15:57:20.430 WARN  MafOutputRenderer - 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=
15:57:20.430 WARN  MafOutputRenderer - 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=
15:57:20.431 WARN  MafOutputRenderer - 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=
15:57:20.431 WARN  MafOutputRenderer - 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=
15:57:20.431 WARN  MafOutputRenderer - 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=
15:57:20.432 WARN  MafOutputRenderer - 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=
15:57:20.432 WARN  MafOutputRenderer - 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=
15:57:20.433 WARN  MafOutputRenderer - 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=
15:57:20.433 WARN  MafOutputRenderer - 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=
15:57:20.433 WARN  MafOutputRenderer - 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=
15:57:20.433 WARN  MafOutputRenderer - 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+
15:57:20.433 WARN  MafOutputRenderer - 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=
15:57:20.434 WARN  MafOutputRenderer - 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=
15:57:20.434 WARN  MafOutputRenderer - 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=
15:57:20.434 WARN  MafOutputRenderer - 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=
15:57:20.434 WARN  MafOutputRenderer - 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=
15:57:20.434 WARN  MafOutputRenderer - 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=
15:57:20.434 WARN  MafOutputRenderer - 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=
15:57:20.435 WARN  MafOutputRenderer - 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=
15:57:20.435 WARN  MafOutputRenderer - 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=
15:57:20.435 WARN  MafOutputRenderer - 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=
15:57:20.435 WARN  MafOutputRenderer - 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=
15:57:20.435 WARN  MafOutputRenderer - 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=
15:57:20.435 WARN  MafOutputRenderer - 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=
15:57:20.436 WARN  MafOutputRenderer - 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=
15:57:20.436 WARN  MafOutputRenderer - 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=
15:57:20.436 WARN  MafOutputRenderer - 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=
15:57:20.436 WARN  MafOutputRenderer - 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=
15:57:20.436 WARN  MafOutputRenderer - 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=
15:57:20.437 WARN  MafOutputRenderer - 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=
15:57:20.437 WARN  MafOutputRenderer - 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=
15:57:20.437 WARN  MafOutputRenderer - 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=
15:57:20.437 WARN  MafOutputRenderer - 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=
15:57:20.437 WARN  MafOutputRenderer - 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=
15:57:20.437 WARN  MafOutputRenderer - 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=
15:57:20.438 WARN  MafOutputRenderer - 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=
15:57:20.438 WARN  MafOutputRenderer - 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=
15:57:20.438 WARN  MafOutputRenderer - 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=
15:57:20.438 WARN  MafOutputRenderer - 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=
15:57:20.438 WARN  MafOutputRenderer - 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=
15:57:20.438 WARN  MafOutputRenderer - 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=
15:57:20.439 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257738 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=
15:57:20.439 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257767 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=
15:57:20.439 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257889-179257890 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=
15:57:20.439 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179257891-179257898 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=
15:57:20.439 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:179258111 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=
15:57:20.440 WARN  MafOutputRenderer - 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=
15:57:20.440 WARN  MafOutputRenderer - 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=
15:57:20.440 WARN  MafOutputRenderer - 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=
15:57:20.440 WARN  MafOutputRenderer - 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=
15:57:20.440 WARN  MafOutputRenderer - 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=
15:57:20.440 WARN  MafOutputRenderer - 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=
15:57:20.441 WARN  MafOutputRenderer - 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=
15:57:20.441 WARN  MafOutputRenderer - 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=
15:57:20.441 WARN  MafOutputRenderer - 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=
15:57:20.441 WARN  MafOutputRenderer - 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=
15:57:20.441 WARN  MafOutputRenderer - 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=
15:57:20.441 WARN  MafOutputRenderer - 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=
15:57:20.442 WARN  MafOutputRenderer - 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=
15:57:20.442 WARN  MafOutputRenderer - 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=
15:57:20.442 WARN  MafOutputRenderer - 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=
15:57:20.442 WARN  MafOutputRenderer - 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=
15:57:20.442 WARN  MafOutputRenderer - 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=
15:57:20.442 WARN  MafOutputRenderer - 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=
15:57:20.443 INFO  ProgressMeter -             unmapped              0.0                   100         206896.6
15:57:20.443 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:57:20.443 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:57:20.443 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:57:20 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:57:20.444 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out13348572936586684743.vcf
15:57:20.597 INFO  Funcotator - ------------------------------------------------------------
15:57:20.597 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:57:20.597 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:57:20.597 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:57:20.597 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:57:20.597 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:57:20 PM GMT
15:57:20.597 INFO  Funcotator - ------------------------------------------------------------
15:57:20.597 INFO  Funcotator - ------------------------------------------------------------
15:57:20.597 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:57:20.597 INFO  Funcotator - Picard Version: 3.4.0
15:57:20.597 INFO  Funcotator - Built for Spark Version: 3.5.0
15:57:20.597 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:57:20.597 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:57:20.597 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:57:20.597 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:57:20.597 INFO  Funcotator - Deflater: IntelDeflater
15:57:20.597 INFO  Funcotator - Inflater: IntelInflater
15:57:20.597 INFO  Funcotator - GCS max retries/reopens: 20
15:57:20.597 INFO  Funcotator - Requester pays: disabled
15:57:20.597 INFO  Funcotator - Initializing engine
15:57:20.598 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
15:57:20.599 INFO  Funcotator - Done initializing engine
15:57:20.599 INFO  Funcotator - Skipping sequence dictionary validation.
15:57:20.599 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:57:20.599 INFO  Funcotator - Initializing data sources...
15:57:20.599 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:57:20.599 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:57:20.599 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
15:57:20.599 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
15:57:20.599 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
15:57:20.599 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:57:20.599 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
15:57:20.599 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:57:20.600 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
15:57:20.600 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
15:57:20.600 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
15:57:20.600 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:57:20.601 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
15:57:20.602 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
15:57:20.603 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
15:57:20.603 INFO  Funcotator - Initializing Funcotator Engine...
15:57:20.603 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:57:20.603 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.
15:57:20.603 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:57:20.604 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9042058572240374317.vcf
15:57:20.604 INFO  ProgressMeter - Starting traversal
15:57:20.604 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:57:20.637 INFO  ProgressMeter -             unmapped              0.0                    57         103636.4
15:57:20.637 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:57:20.637 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:57:20.639 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:57:20 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:57:20.726 INFO  Funcotator - ------------------------------------------------------------
15:57:20.726 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:57:20.726 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:57:20.726 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:57:20.726 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:57:20.726 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:57:20 PM GMT
15:57:20.726 INFO  Funcotator - ------------------------------------------------------------
15:57:20.726 INFO  Funcotator - ------------------------------------------------------------
15:57:20.727 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:57:20.727 INFO  Funcotator - Picard Version: 3.4.0
15:57:20.727 INFO  Funcotator - Built for Spark Version: 3.5.0
15:57:20.727 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:57:20.727 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:57:20.727 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:57:20.727 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:57:20.727 INFO  Funcotator - Deflater: IntelDeflater
15:57:20.727 INFO  Funcotator - Inflater: IntelInflater
15:57:20.727 INFO  Funcotator - GCS max retries/reopens: 20
15:57:20.727 INFO  Funcotator - Requester pays: disabled
15:57:20.727 INFO  Funcotator - Initializing engine
15:57:20.727 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
15:57:20.728 INFO  Funcotator - Done initializing engine
15:57:20.728 INFO  Funcotator - Skipping sequence dictionary validation.
15:57:20.728 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:57:20.728 INFO  Funcotator - Initializing data sources...
15:57:20.728 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:57:20.728 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:57:20.728 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
15:57:20.728 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
15:57:20.728 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
15:57:20.728 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:57:20.728 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
15:57:20.728 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:57:20.729 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
15:57:20.729 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
15:57:20.730 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
15:57:20.730 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:57:20.730 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
15:57:20.731 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
15:57:20.732 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
15:57:20.733 INFO  Funcotator - Initializing Funcotator Engine...
15:57:20.733 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:57:20.733 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.
15:57:20.733 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:57:20.733 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out404383199871452268.maf
15:57:20.733 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
15:57:20.733 INFO  ProgressMeter - Starting traversal
15:57:20.733 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:57:20.735 WARN  MafOutputRenderer - 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=
15:57:20.736 WARN  MafOutputRenderer - 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=
15:57:20.736 WARN  MafOutputRenderer - 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=
15:57:20.736 WARN  MafOutputRenderer - 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=
15:57:20.737 WARN  MafOutputRenderer - 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=
15:57:20.738 WARN  MafOutputRenderer - 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=
15:57:20.738 WARN  MafOutputRenderer - 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=
15:57:20.739 WARN  MafOutputRenderer - 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=
15:57:20.739 WARN  MafOutputRenderer - 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=
15:57:20.740 WARN  MafOutputRenderer - 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=
15:57:20.740 WARN  MafOutputRenderer - 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=
15:57:20.740 WARN  MafOutputRenderer - 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=
15:57:20.741 WARN  MafOutputRenderer - 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=
15:57:20.742 WARN  MafOutputRenderer - 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=
15:57:20.742 WARN  MafOutputRenderer - 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=
15:57:20.743 WARN  MafOutputRenderer - 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=
15:57:20.743 WARN  MafOutputRenderer - 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=
15:57:20.744 WARN  MafOutputRenderer - 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=
15:57:20.744 WARN  MafOutputRenderer - 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=
15:57:20.744 WARN  MafOutputRenderer - 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=
15:57:20.746 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
15:57:20.746 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATAT] attr={} GT=[] filters=
15:57:20.747 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTAT] attr={} GT=[] filters=
15:57:20.748 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTAT] attr={} GT=[] filters=
15:57:20.748 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ACTTGAAGAA] attr={} GT=[] filters=
15:57:20.749 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
15:57:20.750 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATA] attr={} GT=[] filters=
15:57:20.751 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTA] attr={} GT=[] filters=
15:57:20.751 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
15:57:20.752 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
15:57:20.752 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
15:57:20.753 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
15:57:20.754 WARN  MafOutputRenderer - 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=
15:57:20.754 WARN  MafOutputRenderer - 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=
15:57:20.754 WARN  MafOutputRenderer - 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=
15:57:20.756 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
15:57:20.756 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
15:57:20.757 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916621 Q40.00 of type=INDEL alleles=[CTCC*, C] attr={} GT=[] filters=
15:57:20.758 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916622 Q40.00 of type=INDEL alleles=[TCCA*, T] attr={} GT=[] filters=
15:57:20.758 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916623 Q40.00 of type=INDEL alleles=[CCAC*, C] attr={} GT=[] filters=
15:57:20.758 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916624 Q40.00 of type=INDEL alleles=[CACG*, C] attr={} GT=[] filters=
15:57:20.760 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916620 Q40.00 of type=INDEL alleles=[CTC*, C] attr={} GT=[] filters=
15:57:20.760 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916621 Q40.00 of type=INDEL alleles=[TCC*, T] attr={} GT=[] filters=
15:57:20.760 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916622 Q40.00 of type=INDEL alleles=[CCA*, C] attr={} GT=[] filters=
15:57:20.761 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916623 Q40.00 of type=INDEL alleles=[CAC*, C] attr={} GT=[] filters=
15:57:20.762 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916619 Q40.00 of type=INDEL alleles=[CT*, C] attr={} GT=[] filters=
15:57:20.762 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916620 Q40.00 of type=INDEL alleles=[TC*, T] attr={} GT=[] filters=
15:57:20.763 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
15:57:20.763 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
15:57:20.764 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916622 Q40.00 of type=INDEL alleles=[CTCCA*, C] attr={} GT=[] filters=
15:57:20.765 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916623 Q40.00 of type=INDEL alleles=[TCCAC*, T] attr={} GT=[] filters=
15:57:20.765 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916624 Q40.00 of type=INDEL alleles=[CCACG*, C] attr={} GT=[] filters=
15:57:20.765 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916625 Q40.00 of type=INDEL alleles=[CACGA*, C] attr={} GT=[] filters=
15:57:20.767 WARN  MafOutputRenderer - 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=
15:57:20.767 WARN  MafOutputRenderer - 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=
15:57:20.767 WARN  MafOutputRenderer - 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=
15:57:20.768 WARN  MafOutputRenderer - 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=
15:57:20.768 INFO  ProgressMeter -             unmapped              0.0                    57          97714.3
15:57:20.768 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:57:20.768 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:57:20.768 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:57:20 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:57:20.769 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out9042058572240374317.vcf
15:57:20.886 INFO  Funcotator - ------------------------------------------------------------
15:57:20.886 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:57:20.886 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:57:20.886 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:57:20.886 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:57:20.886 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:57:20 PM GMT
15:57:20.886 INFO  Funcotator - ------------------------------------------------------------
15:57:20.886 INFO  Funcotator - ------------------------------------------------------------
15:57:20.887 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:57:20.887 INFO  Funcotator - Picard Version: 3.4.0
15:57:20.887 INFO  Funcotator - Built for Spark Version: 3.5.0
15:57:20.887 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:57:20.887 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:57:20.887 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:57:20.887 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:57:20.887 INFO  Funcotator - Deflater: IntelDeflater
15:57:20.887 INFO  Funcotator - Inflater: IntelInflater
15:57:20.887 INFO  Funcotator - GCS max retries/reopens: 20
15:57:20.887 INFO  Funcotator - Requester pays: disabled
15:57:20.887 INFO  Funcotator - Initializing engine
15:57:20.888 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:57:20.889 INFO  Funcotator - Done initializing engine
15:57:20.889 INFO  Funcotator - Skipping sequence dictionary validation.
15:57:20.889 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:57:20.889 INFO  Funcotator - Initializing data sources...
15:57:20.889 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:57:20.889 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:57:20.889 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
15:57:20.889 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
15:57:20.889 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
15:57:20.889 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:57:20.889 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
15:57:20.889 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:57:20.890 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
15:57:20.890 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
15:57:20.890 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:57:20.891 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:57:20.891 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
15:57:20.892 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
15:57:20.893 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
15:57:20.894 INFO  Funcotator - Initializing Funcotator Engine...
15:57:20.894 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:57:20.894 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
15:57:20.894 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out3656786995212495557.maf
15:57:20.894 INFO  ProgressMeter - Starting traversal
15:57:20.894 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:57:20.897 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178872355 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=
15:57:20.897 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178902506 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=
15:57:20.898 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178907849 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=
15:57:20.898 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178916753 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=
15:57:20.899 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178916791 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=
15:57:20.899 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178921158 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=
15:57:20.900 WARN  MafOutputRenderer - 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=
15:57:20.900 WARN  MafOutputRenderer - 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=
15:57:20.900 WARN  MafOutputRenderer - 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=
15:57:20.901 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178937400 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=
15:57:20.901 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:178947118 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=
15:57:20.902 WARN  MafOutputRenderer - 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=
15:57:20.902 WARN  MafOutputRenderer - 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=
15:57:20.902 WARN  MafOutputRenderer - 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=
15:57:20.902 WARN  MafOutputRenderer - 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=
15:57:20.903 WARN  MafOutputRenderer - 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=
15:57:20.903 WARN  MafOutputRenderer - 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=
15:57:20.903 WARN  MafOutputRenderer - 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=
15:57:20.903 WARN  MafOutputRenderer - 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=
15:57:20.904 WARN  MafOutputRenderer - 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=
15:57:20.904 WARN  MafOutputRenderer - 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=
15:57:20.904 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
15:57:20.904 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:57:20.904 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:57:20.904 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:57:20 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:57:21.000 INFO  Funcotator - ------------------------------------------------------------
15:57:21.000 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:57:21.000 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:57:21.000 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:57:21.000 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:57:21.000 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:57:20 PM GMT
15:57:21.000 INFO  Funcotator - ------------------------------------------------------------
15:57:21.000 INFO  Funcotator - ------------------------------------------------------------
15:57:21.000 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:57:21.000 INFO  Funcotator - Picard Version: 3.4.0
15:57:21.000 INFO  Funcotator - Built for Spark Version: 3.5.0
15:57:21.000 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:57:21.000 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:57:21.000 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:57:21.000 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:57:21.000 INFO  Funcotator - Deflater: IntelDeflater
15:57:21.000 INFO  Funcotator - Inflater: IntelInflater
15:57:21.000 INFO  Funcotator - GCS max retries/reopens: 20
15:57:21.000 INFO  Funcotator - Requester pays: disabled
15:57:21.000 INFO  Funcotator - Initializing engine
15:57:21.001 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
15:57:21.002 INFO  Funcotator - Done initializing engine
15:57:21.002 INFO  Funcotator - Skipping sequence dictionary validation.
15:57:21.002 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:57:21.002 INFO  Funcotator - Initializing data sources...
15:57:21.002 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
15:57:21.002 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:57:21.003 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
15:57:21.003 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
15:57:21.003 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
15:57:21.003 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:57:21.003 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:57:21.003 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
15:57:21.004 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
15:57:21.031 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
15:57:21.031 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:57:21	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:57:21.031 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
15:57:21.031 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:57:21.032 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
15:57:21.032 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
15:57:21.032 INFO  Funcotator - Initializing Funcotator Engine...
15:57:21.032 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:57:21.032 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.
15:57:21.032 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13978577364964129624.vcf
15:57:21.036 INFO  ProgressMeter - Starting traversal
15:57:21.036 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:57:21.040 INFO  ProgressMeter -             unmapped              0.0                    10         150000.0
15:57:21.040 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
15:57:21.040 WARN  Funcotator - ================================================================================
15:57:21.040 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:57:21.040 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:57:21.040 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:57:21.040 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:57:21.040 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:57:21.040 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:57:21.040 WARN  Funcotator - --------------------------------------------------------------------------------
15:57:21.040 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:57:21.040 WARN  Funcotator -  run was misconfigured.     
15:57:21.040 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:57:21.040 WARN  Funcotator - ================================================================================
15:57:21.041 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:57:21 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:57:21.042 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out13978577364964129624.vcf
15:57:21.134 INFO  Funcotator - ------------------------------------------------------------
15:57:21.134 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:57:21.134 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:57:21.134 INFO  Funcotator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:57:21.134 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:57:21.134 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:57:21 PM GMT
15:57:21.134 INFO  Funcotator - ------------------------------------------------------------
15:57:21.135 INFO  Funcotator - ------------------------------------------------------------
15:57:21.135 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:57:21.135 INFO  Funcotator - Picard Version: 3.4.0
15:57:21.135 INFO  Funcotator - Built for Spark Version: 3.5.0
15:57:21.135 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:57:21.135 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:57:21.135 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:57:21.135 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:57:21.135 INFO  Funcotator - Deflater: IntelDeflater
15:57:21.135 INFO  Funcotator - Inflater: IntelInflater
15:57:21.135 INFO  Funcotator - GCS max retries/reopens: 20
15:57:21.135 INFO  Funcotator - Requester pays: disabled
15:57:21.135 INFO  Funcotator - Initializing engine
15:57:21.136 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_multihit_test.vcf
15:57:21.137 INFO  Funcotator - Done initializing engine
15:57:21.137 INFO  Funcotator - Skipping sequence dictionary validation.
15:57:21.137 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:57:21.137 INFO  Funcotator - Initializing data sources...
15:57:21.137 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
15:57:21.137 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:57:21.137 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
15:57:21.137 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
15:57:21.137 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
15:57:21.137 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:57:21.137 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:57:21.138 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
15:57:21.138 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
15:57:21.165 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
15:57:21.165 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:57:21	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:57:21.166 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
15:57:21.166 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:57:21.166 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
15:57:21.167 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
15:57:21.167 INFO  Funcotator - Initializing Funcotator Engine...
15:57:21.167 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:57:21.167 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.
15:57:21.167 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out3539283834485522652.vcf
15:57:21.171 INFO  ProgressMeter - Starting traversal
15:57:21.171 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:57:21.173 INFO  ProgressMeter -             unmapped              0.0                     1          30000.0
15:57:21.173 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:57:21.173 WARN  Funcotator - ================================================================================
15:57:21.173 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:57:21.173 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:57:21.173 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:57:21.173 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:57:21.173 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:57:21.173 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:57:21.173 WARN  Funcotator - --------------------------------------------------------------------------------
15:57:21.173 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:57:21.173 WARN  Funcotator -  run was misconfigured.     
15:57:21.173 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:57:21.173 WARN  Funcotator - ================================================================================
15:57:21.173 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:57:21 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
15:57:21.174 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out3539283834485522652.vcf