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

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

tests
0

failures
0

ignored
1m39.04s

duration
100%

successful

Tests

Test Duration Result
exhaustiveArgumentTest[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8918691360900467997/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null) 1.183s passed
exhaustiveArgumentTest[1](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder17921977485899396791/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null) 1.226s passed
exhaustiveArgumentTest[2](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8918691360900467997/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null) 1.060s passed
exhaustiveArgumentTest[3](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder17921977485899396791/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null) 1.234s passed
exhaustiveArgumentTest[4](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8918691360900467997/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null) 1.109s passed
exhaustiveArgumentTest[5](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder17921977485899396791/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null) 1.159s passed
exhaustiveArgumentTest[6](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8918691360900467997/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null) 1.123s passed
exhaustiveArgumentTest[7](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder17921977485899396791/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null) 1.051s 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) 6.077s 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) 5.543s passed
nonTrivialLargeDataValidationTest[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz, hg19, /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf, [], false) 1.906s 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) 1.911s 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) 12.308s 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) 5.740s 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 0.210s passed
testCanAnnotateMixedContigHg19Clinvar 0.119s passed
testCanAnnotateSpanningDeletions 0.192s passed
testCanCreateNonLocatableFuncotations 1.014s passed
testCanHandleSymbollicAlleleFuncotations 1.152s passed
testCustomVariantClassificationOrder 1.076s passed
testEColiFuncotations 0.131s passed
testEnsureDbSnpInMaf 0.107s passed
testExclusionFromDatasourceVcfToVcf 0.255s passed
testFilterParsing 0.143s passed
testFuncotatorWithoutValidatingResults[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8918691360900467997/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, VCF, null) 0.961s passed
testFuncotatorWithoutValidatingResults[1](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder17921977485899396791/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, VCF, null) 1.010s passed
testFuncotatorWithoutValidatingResults[2](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8918691360900467997/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, VCF, null) 0.956s passed
testFuncotatorWithoutValidatingResults[3](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder17921977485899396791/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, VCF, null) 1.073s passed
testFuncotatorWithoutValidatingResults[4](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8918691360900467997/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, GENE_NAME, MAF, null) 1.021s passed
testFuncotatorWithoutValidatingResults[5](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder17921977485899396791/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, GENE_NAME, MAF, null) 1.164s passed
testFuncotatorWithoutValidatingResults[6](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder8918691360900467997/GRCh37.p13.chr3.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf, ENST00000263967.3, TRANSCRIPT_ID, MAF, null) 1.085s passed
testFuncotatorWithoutValidatingResults[7](/gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, hg19, /tmp/funcotatorTmpFolder17921977485899396791/GRCh37.p13.chr19.fasta, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf, ENST00000397910.4, TRANSCRIPT_ID, MAF, null) 1.156s passed
testMANESelectAnnotationDifferencesAndGencodeV43 0.469s passed
testMafCustomCountFieldsTumorOnly[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields_tumor_only.vcf) 0.149s passed
testMafCustomCountFieldsTumorOnly[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields_tumor_only.vcf) 0.113s passed
testMafCustomCountFields[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf) 0.112s passed
testMafCustomCountFields[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf) 0.115s passed
testManualAnnotationsCorrectness 0.121s passed
testMoreThanOneTNPair 0.097s passed
testNoSpanningDeletionWriteWithMAF 0.162s passed
testNoVariantsProduceMaf 0.102s passed
testSequenceDictionaryCheck 0.119s 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) 5.781s passed
testUserExceptionOnAlleleDepthFieldSizeOneForMafOutput 0.893s passed
testVCFColumnsArentShuffled 0.103s passed
testVCFToMAFPreservesFields 0.110s passed
testVCFToVCFPreservesFields 0.112s passed
testVcfDatasourceAccountsForAltAlleles 0.139s passed
testVcfMafConcordance[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf, /tmp/funcotatorTmpFolder503822256018152464/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 15) 0.212s passed
testVcfMafConcordance[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder503822256018152464/b37.3.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/, true, 57) 0.266s passed
testVcfMafConcordance[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf, /tmp/funcotatorTmpFolder17921977485899396791/GRCh37.p13.chr19.fasta, hg19, [Gencode_19_proteinChange], [Protein_Change], /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/, false, 2057) 33.226s passed
testVcfMafConcordance[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf, /tmp/funcotatorTmpFolder8807599897299512427/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) 0.430s passed
testVcfMafConcordance[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf, /tmp/funcotatorTmpFolder503822256018152464/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) 0.281s passed
testVcfToMafHonorsExcludedFields 0.108s passed
testXsvLocatableAnnotationsHaveCorrectColsForOnlyOnePositionSpecified 0.130s passed
testXsvLocatableAnnotationsHaveOnlyOneEntryForMultiHitLocations 0.132s passed

Standard error

15:07:22.267 INFO  Funcotator - ------------------------------------------------------------
15:07:22.267 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:22.267 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:22.267 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:22.267 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:22.267 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:22 PM GMT
15:07:22.267 INFO  Funcotator - ------------------------------------------------------------
15:07:22.267 INFO  Funcotator - ------------------------------------------------------------
15:07:22.267 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:22.267 INFO  Funcotator - Picard Version: 3.4.0
15:07:22.267 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:22.267 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:22.267 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:22.267 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:22.267 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:22.267 INFO  Funcotator - Deflater: IntelDeflater
15:07:22.267 INFO  Funcotator - Inflater: IntelInflater
15:07:22.268 INFO  Funcotator - GCS max retries/reopens: 20
15:07:22.268 INFO  Funcotator - Requester pays: disabled
15:07:22.268 INFO  Funcotator - Initializing engine
15:07:22.269 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:07:22.270 INFO  Funcotator - Done initializing engine
15:07:22.270 INFO  Funcotator - Skipping sequence dictionary validation.
15:07:22.270 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:22.270 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder11745559209720953387/TranscriptIdFile.txt
15:07:22.271 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:07:22.271 INFO  FuncotatorEngine - Transcript parsing complete.
15:07:22.271 INFO  Funcotator - Initializing data sources...
15:07:22.271 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:22.271 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:22.271 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:22.272 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:22.272 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:22.272 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:22.272 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:22.273 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:22.273 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:22.273 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:22.274 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:22.274 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:22.274 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:22.274 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:22.275 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:22.275 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:22.275 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:22.275 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:22.275 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:22.275 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:22.298 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:22.299 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:22.348 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:22.348 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:22.941 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:22.941 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:22.943 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:22.945 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:22.948 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:22.951 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:22.951 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:22.952 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:22.980 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
15:07:22.980 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
WARNING	2025-05-27 15:07:22	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:22.981 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:23.021 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:23.021 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:23.022 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:23.031 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:23.110 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
15:07:23.110 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:23.111 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:23.111 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:23.219 INFO  Funcotator - Initializing Funcotator Engine...
15:07:23.219 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
15:07:23.220 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:07:23.220 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:07:23.220 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:07:23.220 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:07:23.220 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:07:23.220 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:07:23.221 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:07:23.222 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:07:23.223 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:07:23.223 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:07:23.224 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.3818833337697566065.vcf
15:07:23.224 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
15:07:23.228 INFO  ProgressMeter - Starting traversal
15:07:23.229 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:23.345 INFO  ProgressMeter -             unmapped              0.0                     3           1551.7
15:07:23.345 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:07:23.346 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:07:23.350 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:23 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2296381440
15:07:23.469 INFO  Funcotator - ------------------------------------------------------------
15:07:23.469 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:23.469 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:23.469 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:23.469 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:23.469 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:23 PM GMT
15:07:23.469 INFO  Funcotator - ------------------------------------------------------------
15:07:23.469 INFO  Funcotator - ------------------------------------------------------------
15:07:23.469 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:23.469 INFO  Funcotator - Picard Version: 3.4.0
15:07:23.469 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:23.469 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:23.469 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:23.469 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:23.469 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:23.469 INFO  Funcotator - Deflater: IntelDeflater
15:07:23.469 INFO  Funcotator - Inflater: IntelInflater
15:07:23.469 INFO  Funcotator - GCS max retries/reopens: 20
15:07:23.469 INFO  Funcotator - Requester pays: disabled
15:07:23.469 INFO  Funcotator - Initializing engine
15:07:23.471 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:07:23.472 INFO  Funcotator - Done initializing engine
15:07:23.472 INFO  Funcotator - Skipping sequence dictionary validation.
15:07:23.472 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:23.472 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder997718812391530262/TranscriptIdFile.txt
15:07:23.472 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:07:23.472 INFO  FuncotatorEngine - Transcript parsing complete.
15:07:23.472 INFO  Funcotator - Initializing data sources...
15:07:23.472 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:23.472 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:23.473 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:23.473 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:23.474 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:23.474 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:23.474 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:23.474 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:23.474 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:23.475 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:23.475 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:23.475 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:23.476 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:23.476 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:23.476 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:23.476 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:23.476 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:23.476 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:23.477 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
15:07:23.477 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
15:07:23.500 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:23.501 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:23.549 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:23.550 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:24.145 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:24.145 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:24.146 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:24.149 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:24.152 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:24.154 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:24.154 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:24.155 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:24.182 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:24.182 INFO  DataSourceUtils - 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 15:07:24	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:24.183 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:24.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:24.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:24.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:24.287 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:24.288 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:24.288 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:24.289 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:24.289 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:24.385 INFO  Funcotator - Initializing Funcotator Engine...
15:07:24.385 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:07:24.385 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:07:24.385 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.47459031265959639450.vcf
15:07:24.386 INFO  ProgressMeter - Starting traversal
15:07:24.386 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:24.575 INFO  ProgressMeter -             unmapped              0.0                     4           1269.8
15:07:24.575 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:07:24.575 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:07:24.576 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:24 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2296381440
15:07:24.671 INFO  Funcotator - ------------------------------------------------------------
15:07:24.671 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:24.671 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:24.671 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:24.671 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:24.671 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:24 PM GMT
15:07:24.671 INFO  Funcotator - ------------------------------------------------------------
15:07:24.671 INFO  Funcotator - ------------------------------------------------------------
15:07:24.671 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:24.671 INFO  Funcotator - Picard Version: 3.4.0
15:07:24.671 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:24.671 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:24.671 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:24.671 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:24.671 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:24.671 INFO  Funcotator - Deflater: IntelDeflater
15:07:24.671 INFO  Funcotator - Inflater: IntelInflater
15:07:24.671 INFO  Funcotator - GCS max retries/reopens: 20
15:07:24.671 INFO  Funcotator - Requester pays: disabled
15:07:24.671 INFO  Funcotator - Initializing engine
15:07:24.672 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:07:24.673 INFO  Funcotator - Done initializing engine
15:07:24.673 INFO  Funcotator - Skipping sequence dictionary validation.
15:07:24.673 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:24.673 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder8333027235700308768/TranscriptIdFile.txt
15:07:24.673 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:07:24.673 INFO  FuncotatorEngine - Transcript parsing complete.
15:07:24.673 INFO  Funcotator - Initializing data sources...
15:07:24.673 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:24.673 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:24.674 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:24.674 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:24.674 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
15:07:24.675 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:24.675 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:24.675 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:24.675 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:24.676 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:24.676 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:24.676 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:24.676 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:24.676 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:24.677 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:24.677 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:24.677 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:24.677 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:24.677 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:24.677 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:24.699 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:24.699 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:24.747 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:24.747 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:25.426 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:25.427 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:25.428 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:25.430 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:25.433 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:25.436 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:25.436 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:25.437 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:25.465 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:25.465 INFO  DataSourceUtils - 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 15:07:25	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:25.465 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:25.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:25.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:25.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:25.511 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:25.512 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:25.512 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:25.513 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:25.513 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:25.600 INFO  Funcotator - Initializing Funcotator Engine...
15:07:25.600 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
15:07:25.600 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:07:25.600 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:07:25.600 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:07:25.600 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:07:25.600 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:07:25.600 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:07:25.600 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:07:25.600 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:07:25.600 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:07:25.600 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:07:25.600 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:07:25.600 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:07:25.600 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:07:25.600 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:07:25.601 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:07:25.602 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:07:25.602 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:07:25.602 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.3113833644005720772.vcf
15:07:25.602 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
15:07:25.604 INFO  ProgressMeter - Starting traversal
15:07:25.604 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:25.632 INFO  ProgressMeter -             unmapped              0.0                     3           6428.6
15:07:25.632 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:07:25.632 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:07:25.635 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:25 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2296381440
15:07:25.734 INFO  Funcotator - ------------------------------------------------------------
15:07:25.734 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:25.734 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:25.734 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:25.734 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:25.734 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:25 PM GMT
15:07:25.734 INFO  Funcotator - ------------------------------------------------------------
15:07:25.734 INFO  Funcotator - ------------------------------------------------------------
15:07:25.734 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:25.734 INFO  Funcotator - Picard Version: 3.4.0
15:07:25.734 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:25.734 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:25.734 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:25.734 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:25.734 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:25.734 INFO  Funcotator - Deflater: IntelDeflater
15:07:25.734 INFO  Funcotator - Inflater: IntelInflater
15:07:25.734 INFO  Funcotator - GCS max retries/reopens: 20
15:07:25.734 INFO  Funcotator - Requester pays: disabled
15:07:25.734 INFO  Funcotator - Initializing engine
15:07:25.735 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:07:25.736 INFO  Funcotator - Done initializing engine
15:07:25.736 INFO  Funcotator - Skipping sequence dictionary validation.
15:07:25.736 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:25.736 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder2216922708723739378/TranscriptIdFile.txt
15:07:25.736 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:07:25.736 INFO  FuncotatorEngine - Transcript parsing complete.
15:07:25.736 INFO  Funcotator - Initializing data sources...
15:07:25.736 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:25.736 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:25.737 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:25.737 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:25.737 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:25.738 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:25.738 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:25.738 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:25.738 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:25.738 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:25.739 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:25.739 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:25.739 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:25.739 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:25.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:25.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:25.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:25.740 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:25.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:25.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:25.763 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:25.764 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:25.812 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:25.812 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
15:07:26.536 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:26.536 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:26.537 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:26.540 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:26.543 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:26.546 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:26.546 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:26.547 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:26.574 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:26.574 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:07:26	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:26.575 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:26.613 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:26.613 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:26.614 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:26.621 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:26.622 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:26.622 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:26.623 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:26.623 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:26.752 INFO  Funcotator - Initializing Funcotator Engine...
15:07:26.753 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:07:26.753 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:07:26.753 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.410178262496035210119.vcf
15:07:26.754 INFO  ProgressMeter - Starting traversal
15:07:26.755 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:26.869 INFO  ProgressMeter -             unmapped              0.0                     4           2105.3
15:07:26.870 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:07:26.870 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:07:26.870 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2430599168
15:07:27.008 INFO  Funcotator - ------------------------------------------------------------
15:07:27.008 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:27.008 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:27.008 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:27.008 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:27.008 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:27 PM GMT
15:07:27.008 INFO  Funcotator - ------------------------------------------------------------
15:07:27.008 INFO  Funcotator - ------------------------------------------------------------
15:07:27.008 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:27.009 INFO  Funcotator - Picard Version: 3.4.0
15:07:27.009 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:27.009 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:27.009 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:27.009 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:27.009 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:27.009 INFO  Funcotator - Deflater: IntelDeflater
15:07:27.009 INFO  Funcotator - Inflater: IntelInflater
15:07:27.009 INFO  Funcotator - GCS max retries/reopens: 20
15:07:27.009 INFO  Funcotator - Requester pays: disabled
15:07:27.009 INFO  Funcotator - Initializing engine
15:07:27.010 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:07:27.010 INFO  Funcotator - Done initializing engine
15:07:27.010 INFO  Funcotator - Skipping sequence dictionary validation.
15:07:27.010 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:27.010 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder9997460109814525749/TranscriptIdFile.txt
15:07:27.010 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:07:27.010 INFO  FuncotatorEngine - Transcript parsing complete.
15:07:27.010 INFO  Funcotator - Initializing data sources...
15:07:27.010 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:27.010 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:27.011 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:27.011 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:27.011 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:27.012 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:27.012 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:27.012 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:27.012 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:27.012 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:27.013 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:27.013 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:27.013 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:27.013 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:27.013 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:27.014 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:27.014 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:27.014 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:27.014 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:27.014 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:27.036 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
15:07:27.036 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:27.155 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:27.156 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:27.739 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:27.739 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:27.740 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:27.742 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:27.745 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:27.747 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:27.747 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:27.748 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:27.775 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:27.775 INFO  DataSourceUtils - 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 15:07:27	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:27.776 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:27.814 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:27.814 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:27.815 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:27.822 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:27.822 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:27.822 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:27.823 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:27.824 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:27.904 INFO  Funcotator - Initializing Funcotator Engine...
15:07:27.904 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
15:07:27.905 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:07:27.905 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:07:27.905 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:07:27.905 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:07:27.906 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:07:27.906 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:07:27.906 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:07:27.906 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000263967.38211925585842279742.maf
15:07:27.908 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
15:07:27.910 INFO  ProgressMeter - Starting traversal
15:07:27.910 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:27.979 INFO  ProgressMeter -             unmapped              0.0                     3           2608.7
15:07:27.979 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:07:27.979 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:07:27.979 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:27 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2430599168
15:07:28.070 INFO  Funcotator - ------------------------------------------------------------
15:07:28.071 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:28.071 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:28.071 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:28.071 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:28.071 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:28 PM GMT
15:07:28.071 INFO  Funcotator - ------------------------------------------------------------
15:07:28.071 INFO  Funcotator - ------------------------------------------------------------
15:07:28.071 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:28.071 INFO  Funcotator - Picard Version: 3.4.0
15:07:28.071 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:28.071 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:28.071 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:28.071 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:28.071 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:28.071 INFO  Funcotator - Deflater: IntelDeflater
15:07:28.071 INFO  Funcotator - Inflater: IntelInflater
15:07:28.071 INFO  Funcotator - GCS max retries/reopens: 20
15:07:28.071 INFO  Funcotator - Requester pays: disabled
15:07:28.071 INFO  Funcotator - Initializing engine
15:07:28.072 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:07:28.073 INFO  Funcotator - Done initializing engine
15:07:28.073 INFO  Funcotator - Skipping sequence dictionary validation.
15:07:28.073 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:28.073 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder17218515064708580695/TranscriptIdFile.txt
15:07:28.073 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:07:28.073 INFO  FuncotatorEngine - Transcript parsing complete.
15:07:28.073 INFO  Funcotator - Initializing data sources...
15:07:28.073 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:28.073 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:28.074 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:28.074 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:28.074 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:28.074 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:28.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:28.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:28.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:28.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:28.075 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:28.076 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:28.076 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:28.076 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:28.076 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:28.077 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:28.077 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:28.077 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:28.077 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:28.077 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:28.102 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:28.102 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:28.148 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:28.149 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:28.822 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:28.822 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:28.823 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:28.825 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
15:07:28.828 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:28.831 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:28.832 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:28.832 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:28.873 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
15:07:28.874 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:07:28	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:28.874 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:28.938 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:28.938 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:28.938 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:28.946 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:28.946 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:28.946 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:28.947 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:28.947 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:29.028 INFO  Funcotator - Initializing Funcotator Engine...
15:07:29.029 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:07:29.029 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:07:29.029 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_GENE_NAME_ENST00000397910.48739442592404035529.maf
15:07:29.029 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
15:07:29.030 INFO  ProgressMeter - Starting traversal
15:07:29.030 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:29.139 INFO  ProgressMeter -             unmapped              0.0                     4           2201.8
15:07:29.139 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:07:29.139 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:07:29.139 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:29 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2577399808
15:07:29.275 INFO  Funcotator - ------------------------------------------------------------
15:07:29.275 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:29.275 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:29.275 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:29.275 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:29.275 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:29 PM GMT
15:07:29.275 INFO  Funcotator - ------------------------------------------------------------
15:07:29.275 INFO  Funcotator - ------------------------------------------------------------
15:07:29.275 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:29.275 INFO  Funcotator - Picard Version: 3.4.0
15:07:29.275 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:29.275 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:29.275 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:29.275 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:29.275 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:29.275 INFO  Funcotator - Deflater: IntelDeflater
15:07:29.275 INFO  Funcotator - Inflater: IntelInflater
15:07:29.275 INFO  Funcotator - GCS max retries/reopens: 20
15:07:29.275 INFO  Funcotator - Requester pays: disabled
15:07:29.275 INFO  Funcotator - Initializing engine
15:07:29.276 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:07:29.277 INFO  Funcotator - Done initializing engine
15:07:29.277 INFO  Funcotator - Skipping sequence dictionary validation.
15:07:29.277 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:29.277 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder18436230619566444923/TranscriptIdFile.txt
15:07:29.277 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000263967.3
15:07:29.277 INFO  FuncotatorEngine - Transcript parsing complete.
15:07:29.277 INFO  Funcotator - Initializing data sources...
15:07:29.277 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:29.277 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:29.278 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:29.278 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:29.278 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:29.278 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:29.278 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:29.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:29.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:29.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:29.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:29.279 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:29.280 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:29.280 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:29.280 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:29.280 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:29.280 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:29.280 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:29.280 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:29.281 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:29.301 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:29.302 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:29.349 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:29.350 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:30.055 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
15:07:30.055 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:30.056 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:30.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:30.062 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:30.064 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:30.064 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
15:07:30.065 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:30.092 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
15:07:30.092 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 15:07:30	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:30.092 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
15:07:30.130 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:30.130 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:30.131 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
15:07:30.138 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:30.139 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:30.139 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:30.140 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:30.140 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:30.227 INFO  Funcotator - Initializing Funcotator Engine...
15:07:30.227 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
15:07:30.228 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:07:30.228 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:07:30.228 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:07:30.228 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:07:30.228 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:07:30.228 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000263967.37853025683557260794.maf
15:07:30.229 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
15:07:30.231 INFO  ProgressMeter - Starting traversal
15:07:30.231 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:30.263 INFO  ProgressMeter -             unmapped              0.0                     3           5625.0
15:07:30.263 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:07:30.263 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:07:30.263 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:30 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2650800128
15:07:30.353 INFO  Funcotator - ------------------------------------------------------------
15:07:30.353 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:30.353 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:30.353 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:30.353 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:30.353 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:30 PM GMT
15:07:30.353 INFO  Funcotator - ------------------------------------------------------------
15:07:30.353 INFO  Funcotator - ------------------------------------------------------------
15:07:30.353 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:30.353 INFO  Funcotator - Picard Version: 3.4.0
15:07:30.353 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:30.353 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:30.353 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:30.353 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:30.353 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:30.353 INFO  Funcotator - Deflater: IntelDeflater
15:07:30.353 INFO  Funcotator - Inflater: IntelInflater
15:07:30.353 INFO  Funcotator - GCS max retries/reopens: 20
15:07:30.353 INFO  Funcotator - Requester pays: disabled
15:07:30.353 INFO  Funcotator - Initializing engine
15:07:30.354 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:07:30.355 INFO  Funcotator - Done initializing engine
15:07:30.355 INFO  Funcotator - Skipping sequence dictionary validation.
15:07:30.355 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:30.355 INFO  FuncotatorEngine - Opened transcript file: /tmp/nonExistentFileHolder10694619312166004412/TranscriptIdFile.txt
15:07:30.355 INFO  FuncotatorEngine -     Adding transcript ID to transcript set: ENST00000397910.4
15:07:30.355 INFO  FuncotatorEngine - Transcript parsing complete.
15:07:30.355 INFO  Funcotator - Initializing data sources...
15:07:30.355 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:30.355 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:30.355 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:30.355 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:30.356 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
15:07:30.356 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:30.356 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:30.356 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:30.356 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:30.357 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:30.357 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:30.357 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:30.357 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:30.357 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:30.358 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:30.358 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:30.358 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:30.358 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:30.358 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:30.358 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:30.379 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:30.379 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:30.426 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:30.426 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:31.043 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:31.043 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:31.044 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:31.046 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:31.049 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:31.051 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:31.051 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
15:07:31.051 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:31.079 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:31.079 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:07:31	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:31.080 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:31.117 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:31.118 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:31.118 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:31.125 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:31.126 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:31.126 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:31.127 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:31.127 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:31.207 INFO  Funcotator - Initializing Funcotator Engine...
15:07:31.207 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:07:31.207 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:07:31.207 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out_TRANSCRIPT_ID_ENST00000397910.48991247860837217605.maf
15:07:31.207 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
15:07:31.209 INFO  ProgressMeter - Starting traversal
15:07:31.209 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:31.313 INFO  ProgressMeter -             unmapped              0.0                     4           2307.7
15:07:31.313 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:07:31.313 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:07:31.314 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:31 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2650800128
15:07:31.437 INFO  Funcotator - ------------------------------------------------------------
15:07:31.437 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:31.437 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:31.437 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:31.437 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:31.438 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:31 PM GMT
15:07:31.438 INFO  Funcotator - ------------------------------------------------------------
15:07:31.438 INFO  Funcotator - ------------------------------------------------------------
15:07:31.438 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:31.438 INFO  Funcotator - Picard Version: 3.4.0
15:07:31.438 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:31.438 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:31.438 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:31.438 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:31.438 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:31.438 INFO  Funcotator - Deflater: IntelDeflater
15:07:31.438 INFO  Funcotator - Inflater: IntelInflater
15:07:31.438 INFO  Funcotator - GCS max retries/reopens: 20
15:07:31.438 INFO  Funcotator - Requester pays: disabled
15:07:31.438 INFO  Funcotator - Initializing engine
15:07:31.440 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
15:07:31.442 INFO  Funcotator - Done initializing engine
15:07:31.442 INFO  Funcotator - Validating sequence dictionaries...
15:07:31.442 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:31.442 INFO  Funcotator - Initializing data sources...
15:07:31.442 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:31.442 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:31.442 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:31.443 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:31.443 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:31.443 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:31.443 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:31.443 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:31.444 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:31.444 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:31.444 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:31.444 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:31.444 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:31.445 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:31.445 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:31.445 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:31.445 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:31.445 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:31.445 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
15:07:31.446 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:31.466 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:31.467 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:31.513 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
15:07:31.514 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:32.050 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:32.050 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:32.052 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:32.054 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:32.057 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:32.059 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:32.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:32.060 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:32.087 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
15:07:32.087 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
WARNING	2025-05-27 15:07:32	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:32.087 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:32.184 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:32.184 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:32.184 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:32.191 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:32.192 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:32.192 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:32.193 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:32.193 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:32.273 INFO  Funcotator - Initializing Funcotator Engine...
15:07:32.273 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:07:32.273 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.
15:07:32.273 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator2647832705245132819.vcf
15:07:32.276 INFO  ProgressMeter - Starting traversal
15:07:32.276 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:34.371 INFO  ProgressMeter -             unmapped              0.0                   198           5670.6
15:07:34.371 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:07:34.371 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:07:34.382 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:34 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2650800128
15:07:34.383 WARN  gatk -   VCF Elapsed Time: 3.067365066s
15:07:34.384 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet1.vcf.funcotator2647832705245132819.vcf
15:07:34.387 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
15:07:34.498 INFO  Funcotator - ------------------------------------------------------------
15:07:34.498 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:34.498 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:34.498 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:34.498 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:34.498 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:34 PM GMT
15:07:34.498 INFO  Funcotator - ------------------------------------------------------------
15:07:34.498 INFO  Funcotator - ------------------------------------------------------------
15:07:34.498 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:34.498 INFO  Funcotator - Picard Version: 3.4.0
15:07:34.498 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:34.498 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:34.498 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:34.498 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:34.498 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:34.498 INFO  Funcotator - Deflater: IntelDeflater
15:07:34.498 INFO  Funcotator - Inflater: IntelInflater
15:07:34.498 INFO  Funcotator - GCS max retries/reopens: 20
15:07:34.498 INFO  Funcotator - Requester pays: disabled
15:07:34.498 INFO  Funcotator - Initializing engine
15:07:34.501 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
15:07:34.502 INFO  Funcotator - Done initializing engine
15:07:34.502 INFO  Funcotator - Validating sequence dictionaries...
15:07:34.502 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:34.502 INFO  Funcotator - Initializing data sources...
15:07:34.502 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:34.503 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:34.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:34.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:34.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:34.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:34.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:34.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:34.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:34.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:34.505 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:34.505 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:34.505 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:34.505 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:34.505 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:34.506 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:34.506 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
15:07:34.506 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:34.506 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:34.506 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:34.527 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:34.528 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:34.576 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:34.577 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:35.174 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:35.175 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:35.176 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:35.178 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:35.180 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:35.182 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:35.183 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:35.183 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:35.210 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:35.210 INFO  DataSourceUtils - 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 15:07:35	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:35.211 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:35.249 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:35.249 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:35.249 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:35.256 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:35.257 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:35.257 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:35.258 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:35.258 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:35.339 INFO  Funcotator - Initializing Funcotator Engine...
15:07:35.339 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:07:35.339 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.
15:07:35.339 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator8565973621186613827.maf
15:07:35.339 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
15:07:35.341 INFO  ProgressMeter - Starting traversal
15:07:35.341 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:37.389 INFO  ProgressMeter -             unmapped              0.0                   198           5800.8
15:07:37.389 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:07:37.389 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:07:37.389 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:37 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2650800128
15:07:37.390 WARN  gatk -   MAF Elapsed Time: 2.998664038s
15:07:37.497 INFO  Funcotator - ------------------------------------------------------------
15:07:37.497 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:37.497 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:37.497 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:37.497 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:37.497 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:37 PM GMT
15:07:37.497 INFO  Funcotator - ------------------------------------------------------------
15:07:37.497 INFO  Funcotator - ------------------------------------------------------------
15:07:37.497 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:37.497 INFO  Funcotator - Picard Version: 3.4.0
15:07:37.497 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:37.497 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:37.497 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:37.497 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:37.497 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:37.497 INFO  Funcotator - Deflater: IntelDeflater
15:07:37.497 INFO  Funcotator - Inflater: IntelInflater
15:07:37.497 INFO  Funcotator - GCS max retries/reopens: 20
15:07:37.497 INFO  Funcotator - Requester pays: disabled
15:07:37.497 INFO  Funcotator - Initializing engine
15:07:37.500 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
15:07:37.501 INFO  Funcotator - Done initializing engine
15:07:37.501 INFO  Funcotator - Validating sequence dictionaries...
15:07:37.501 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:37.501 INFO  Funcotator - Initializing data sources...
15:07:37.501 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:37.501 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:37.502 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:37.502 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:37.502 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:37.502 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:37.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:37.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:37.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:37.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:37.503 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:37.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:37.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:37.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:37.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:37.504 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
15:07:37.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:37.504 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:37.504 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:37.505 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:37.526 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:37.527 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:37.575 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:37.576 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:38.123 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:38.123 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:38.124 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:38.127 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:38.130 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:38.132 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:38.132 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:38.133 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:38.161 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
15:07:38.161 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
WARNING	2025-05-27 15:07:38	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:38.161 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
15:07:38.201 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:38.201 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
15:07:38.201 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
15:07:38.210 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:38.210 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:38.210 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:38.211 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:38.212 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:38.361 INFO  Funcotator - Initializing Funcotator Engine...
15:07:38.362 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:07:38.362 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.
15:07:38.362 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator11495322811355185010.vcf
15:07:38.364 INFO  ProgressMeter - Starting traversal
15:07:38.364 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:39.321 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:07:39.321 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:07:40.106 INFO  ProgressMeter -             unmapped              0.0                   168           5786.5
15:07:40.106 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
15:07:40.106 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
15:07:40.112 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:40 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=2650800128
15:07:40.112 WARN  gatk -   VCF Elapsed Time: 2.719672088s
15:07:40.113 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSet2.vcf.funcotator11495322811355185010.vcf
15:07:40.115 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2_expected.vcf
15:07:40.210 INFO  Funcotator - ------------------------------------------------------------
15:07:40.210 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:40.210 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:40.210 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:40.210 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:40.210 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:40 PM GMT
15:07:40.210 INFO  Funcotator - ------------------------------------------------------------
15:07:40.210 INFO  Funcotator - ------------------------------------------------------------
15:07:40.210 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:40.210 INFO  Funcotator - Picard Version: 3.4.0
15:07:40.210 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:40.210 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:40.210 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:40.210 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:40.210 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:40.210 INFO  Funcotator - Deflater: IntelDeflater
15:07:40.210 INFO  Funcotator - Inflater: IntelInflater
15:07:40.210 INFO  Funcotator - GCS max retries/reopens: 20
15:07:40.210 INFO  Funcotator - Requester pays: disabled
15:07:40.210 INFO  Funcotator - Initializing engine
15:07:40.212 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet2.vcf
15:07:40.213 INFO  Funcotator - Done initializing engine
15:07:40.213 INFO  Funcotator - Validating sequence dictionaries...
15:07:40.214 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:40.214 INFO  Funcotator - Initializing data sources...
15:07:40.214 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:40.214 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:40.214 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:40.214 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:40.214 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:40.215 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:40.215 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:40.215 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:40.215 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:40.215 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:40.216 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
15:07:40.216 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:40.216 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:40.216 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:40.216 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:40.216 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:40.217 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:40.217 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:40.217 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:40.217 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:40.237 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:40.238 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:40.285 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:40.286 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:40.911 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:40.912 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:40.913 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:40.916 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:40.918 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:40.920 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:40.921 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:40.921 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:40.948 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:40.949 INFO  DataSourceUtils - 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 15:07:40	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:40.949 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:40.987 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:40.987 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:40.987 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
15:07:40.995 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:40.995 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:40.995 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:40.996 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:40.996 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:41.077 INFO  Funcotator - Initializing Funcotator Engine...
15:07:41.078 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:07:41.078 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.
15:07:41.078 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet2.vcf.funcotator6818102644405780837.maf
15:07:41.078 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
15:07:41.079 INFO  ProgressMeter - Starting traversal
15:07:41.079 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:42.229 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:07:42.229 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:50884775-50884775 due to alternate allele: *
15:07:42.933 INFO  ProgressMeter -             unmapped              0.0                   168           5436.9
15:07:42.933 INFO  ProgressMeter - Traversal complete. Processed 168 total variants in 0.0 minutes.
15:07:42.933 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/150
15:07:42.933 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:42 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3019898880
15:07:42.933 WARN  gatk -   MAF Elapsed Time: 2.813671883s
15:07:43.026 INFO  Funcotator - ------------------------------------------------------------
15:07:43.026 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:43.026 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:43.026 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:43.026 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:43.026 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:43 PM GMT
15:07:43.026 INFO  Funcotator - ------------------------------------------------------------
15:07:43.026 INFO  Funcotator - ------------------------------------------------------------
15:07:43.026 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:43.026 INFO  Funcotator - Picard Version: 3.4.0
15:07:43.026 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:43.026 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:43.026 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:43.026 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:43.026 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:43.026 INFO  Funcotator - Deflater: IntelDeflater
15:07:43.026 INFO  Funcotator - Inflater: IntelInflater
15:07:43.026 INFO  Funcotator - GCS max retries/reopens: 20
15:07:43.026 INFO  Funcotator - Requester pays: disabled
15:07:43.026 INFO  Funcotator - Initializing engine
15:07:43.028 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
15:07:43.029 INFO  Funcotator - Done initializing engine
15:07:43.029 INFO  Funcotator - Validating sequence dictionaries...
15:07:43.030 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:43.030 INFO  Funcotator - Initializing data sources...
15:07:43.030 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:43.030 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:43.030 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:43.030 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:43.031 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:43.031 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:43.031 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:43.031 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:43.031 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:43.031 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
15:07:43.032 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:43.032 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:43.032 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:43.032 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:43.041 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:43.041 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:43.041 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:43.041 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:43.041 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:43.041 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:43.062 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:43.062 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:43.109 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:43.110 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:43.662 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:43.663 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:43.663 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:43.665 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
15:07:43.668 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:43.670 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:43.670 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:43.671 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:43.698 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:43.698 INFO  DataSourceUtils - 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 15:07:43	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:43.698 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:43.737 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:43.737 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:43.738 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:43.745 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:43.745 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:43.745 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:43.746 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:43.747 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:43.891 INFO  Funcotator - Initializing Funcotator Engine...
15:07:43.891 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:07:43.891 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
15:07:43.891 INFO  Funcotator - Creating a VCF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator12915439883355719015.vcf
15:07:43.893 INFO  ProgressMeter - Starting traversal
15:07:43.893 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:43.903 INFO  ProgressMeter -             unmapped              0.0                     1           6000.0
15:07:43.903 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:07:43.903 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:07:43.904 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:43 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3019898880
15:07:43.904 WARN  gatk -   VCF Elapsed Time: 0.968733837s
15:07:43.905 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/hashSetOrderingIssue.vcf.funcotator12915439883355719015.vcf
15:07:43.906 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue_expected.vcf
15:07:43.996 INFO  Funcotator - ------------------------------------------------------------
15:07:43.996 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:43.996 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:43.996 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:43.996 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:43.996 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:43 PM GMT
15:07:43.996 INFO  Funcotator - ------------------------------------------------------------
15:07:43.996 INFO  Funcotator - ------------------------------------------------------------
15:07:43.996 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:43.996 INFO  Funcotator - Picard Version: 3.4.0
15:07:43.996 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:43.996 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:43.996 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:43.996 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:43.996 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:43.996 INFO  Funcotator - Deflater: IntelDeflater
15:07:43.996 INFO  Funcotator - Inflater: IntelInflater
15:07:43.996 INFO  Funcotator - GCS max retries/reopens: 20
15:07:43.996 INFO  Funcotator - Requester pays: disabled
15:07:43.996 INFO  Funcotator - Initializing engine
15:07:43.999 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf
15:07:44.000 INFO  Funcotator - Done initializing engine
15:07:44.000 INFO  Funcotator - Validating sequence dictionaries...
15:07:44.000 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:44.000 INFO  Funcotator - Initializing data sources...
15:07:44.000 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:44.000 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:44.000 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:44.000 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:44.001 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:44.001 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:44.001 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:44.001 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:44.001 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:44.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:44.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:44.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:44.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:44.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:44.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:44.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:44.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:44.003 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:44.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:44.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:44.023 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:44.024 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:44.071 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:44.071 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:44.665 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
15:07:44.665 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:44.666 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:44.668 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
15:07:44.671 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:44.673 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:44.673 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
15:07:44.674 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:44.701 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:44.701 INFO  DataSourceUtils - 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 15:07:44	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:44.701 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:44.739 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:44.739 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:44.740 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:44.747 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:44.747 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:44.747 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:44.748 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:44.749 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:44.828 INFO  Funcotator - Initializing Funcotator Engine...
15:07:44.828 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:07:44.828 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.
15:07:44.829 INFO  Funcotator - Creating a MAF file for output: file:/tmp/hashSetOrderingIssue.vcf.funcotator12223524335269164447.maf
15:07:44.829 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
15:07:44.830 INFO  ProgressMeter - Starting traversal
15:07:44.830 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:44.840 INFO  ProgressMeter -             unmapped              0.0                     1           6000.0
15:07:44.840 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:07:44.840 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:07:44.840 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:44 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3019898880
15:07:44.840 WARN  gatk -   MAF Elapsed Time: 0.933139606s
15:07:44.938 INFO  Funcotator - ------------------------------------------------------------
15:07:44.938 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:44.938 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:44.938 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:44.938 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:44.938 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:44 PM GMT
15:07:44.938 INFO  Funcotator - ------------------------------------------------------------
15:07:44.938 INFO  Funcotator - ------------------------------------------------------------
15:07:44.938 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:44.938 INFO  Funcotator - Picard Version: 3.4.0
15:07:44.938 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:44.938 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:44.938 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:44.938 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:44.938 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:44.938 INFO  Funcotator - Deflater: IntelDeflater
15:07:44.938 INFO  Funcotator - Inflater: IntelInflater
15:07:44.938 INFO  Funcotator - GCS max retries/reopens: 20
15:07:44.938 INFO  Funcotator - Requester pays: disabled
15:07:44.938 INFO  Funcotator - Initializing engine
15:07:44.981 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
15:07:45.002 INFO  Funcotator - Done initializing engine
15:07:45.002 INFO  Funcotator - Validating sequence dictionaries...
15:07:45.009 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:45.009 INFO  Funcotator - Initializing data sources...
15:07:45.009 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:45.009 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:45.010 INFO  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
15:07:45.010 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
15:07:45.010 INFO  DataSourceUtils - Resolved data source 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
15:07:45.010 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
15:07:45.011 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
15:07:45.011 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
15:07:45.011 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
15:07:45.011 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
15:07:45.011 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
15:07:45.012 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
15:07:45.012 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
15:07:45.012 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
15:07:45.012 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
15:07:45.012 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:45.012 INFO  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
15:07:45.013 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
15:07:45.032 INFO  DataSourceUtils - Resolved data source 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
15:07:45.033 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
15:07:45.079 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
15:07:45.080 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
15:07:45.648 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
15:07:45.648 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:45.649 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:07:45.650 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
15:07:45.652 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:07:45.653 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
15:07:45.719 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
15:07:45.719 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
15:07:45.719 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
15:07:45.727 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
15:07:45.727 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:45.728 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
15:07:45.728 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
15:07:45.729 INFO  Funcotator - Initializing Funcotator Engine...
15:07:45.733 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:07:45.733 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator14153039155528775078.vcf
15:07:45.751 INFO  ProgressMeter - Starting traversal
15:07:45.751 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:45.781 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.
15:07:45.784 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
15:07:45.788 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:07:45.792 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:07:45.792 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:07:45.792 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:07:45.792 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:07:45.792 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:07:45.794 INFO  ProgressMeter -             unmapped              0.0                     5           6976.7
15:07:45.794 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
15:07:45.794 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:07:45.805 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:45 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3019898880
15:07:45.805 WARN  gatk -   VCF Elapsed Time: 0.964277608s
15:07:45.806 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestVariantSetHG38.vcf.funcotator14153039155528775078.vcf
15:07:45.816 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38_expected.vcf
15:07:45.924 INFO  Funcotator - ------------------------------------------------------------
15:07:45.925 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:45.925 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:45.925 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:45.925 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:45.925 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:45 PM GMT
15:07:45.925 INFO  Funcotator - ------------------------------------------------------------
15:07:45.925 INFO  Funcotator - ------------------------------------------------------------
15:07:45.925 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:45.925 INFO  Funcotator - Picard Version: 3.4.0
15:07:45.925 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:45.925 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:45.925 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:45.925 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:45.925 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:45.925 INFO  Funcotator - Deflater: IntelDeflater
15:07:45.925 INFO  Funcotator - Inflater: IntelInflater
15:07:45.925 INFO  Funcotator - GCS max retries/reopens: 20
15:07:45.925 INFO  Funcotator - Requester pays: disabled
15:07:45.925 INFO  Funcotator - Initializing engine
15:07:45.950 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSetHG38.vcf
15:07:45.972 INFO  Funcotator - Done initializing engine
15:07:45.972 INFO  Funcotator - Validating sequence dictionaries...
15:07:45.978 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:45.978 INFO  Funcotator - Initializing data sources...
15:07:45.978 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:45.979 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:45.979 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
15:07:45.979 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
15:07:45.979 INFO  DataSourceUtils - Resolved data source 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
15:07:45.980 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38/hgnc_download_Nov302017.tsv
15:07:45.980 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg38/cosmic_fusion.tsv
15:07:45.980 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
15:07:45.980 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
15:07:45.980 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
15:07:45.981 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
15:07:45.981 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
15:07:45.981 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
15:07:45.981 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
15:07:45.981 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
15:07:45.981 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:45.981 INFO  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
15:07:45.982 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
15:07:46.002 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/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:46.002 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
15:07:46.048 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
15:07:46.049 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
15:07:46.624 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg38.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:07:46.624 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:46.625 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:07:46.626 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
15:07:46.628 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:07:46.629 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
15:07:46.694 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
15:07:46.695 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
15:07:46.695 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
15:07:46.702 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
15:07:46.703 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:46.703 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
15:07:46.704 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v28.regressionTestVariantSet.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.pc_transcripts.fa
15:07:46.705 INFO  Funcotator - Initializing Funcotator Engine...
15:07:46.708 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:07:46.708 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSetHG38.vcf.funcotator17138147003230142762.maf
15:07:46.710 INFO  ProgressMeter - Starting traversal
15:07:46.710 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:46.740 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.
15:07:46.741 WARN  GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000374877.7 for problem variant: chr17:80090386-80090449(CAGCACGTGCATGAACAACACAGGACACACACAGCACGTGCATGAACAACACAGGACACACACA* -> C)
15:07:46.743 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:07:46.748 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:07:46.748 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DEL>
15:07:46.749 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:07:46.749 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:07:46.749 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr17:81902450-81902500 due to alternate allele: <DUP>
15:07:46.750 INFO  ProgressMeter -             unmapped              0.0                     5           7500.0
15:07:46.750 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
15:07:46.750 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:07:46.750 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:46 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3019898880
15:07:46.751 WARN  gatk -   MAF Elapsed Time: 0.922335932s
15:07:46.847 INFO  Funcotator - ------------------------------------------------------------
15:07:46.847 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:46.847 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:46.847 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:46.847 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:46.847 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:46 PM GMT
15:07:46.847 INFO  Funcotator - ------------------------------------------------------------
15:07:46.847 INFO  Funcotator - ------------------------------------------------------------
15:07:46.847 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:46.847 INFO  Funcotator - Picard Version: 3.4.0
15:07:46.847 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:46.847 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:46.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:46.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:46.847 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:46.847 INFO  Funcotator - Deflater: IntelDeflater
15:07:46.847 INFO  Funcotator - Inflater: IntelInflater
15:07:46.847 INFO  Funcotator - GCS max retries/reopens: 20
15:07:46.847 INFO  Funcotator - Requester pays: disabled
15:07:46.847 INFO  Funcotator - Initializing engine
15:07:46.850 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
15:07:46.851 INFO  Funcotator - Done initializing engine
15:07:46.851 INFO  Funcotator - Validating sequence dictionaries...
15:07:46.852 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:46.852 INFO  Funcotator - Initializing data sources...
15:07:46.852 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:46.852 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:46.852 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:46.852 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:46.852 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:46.853 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:46.853 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:46.853 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:46.853 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:46.853 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:46.854 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:46.854 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:46.854 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:46.854 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:46.855 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:46.855 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:46.855 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:46.855 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:46.855 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:46.855 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:46.875 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:46.876 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:46.922 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:46.923 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:47.467 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:47.467 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:47.468 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:47.470 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:47.473 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:47.475 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:47.475 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:47.476 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:47.506 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:47.506 INFO  DataSourceUtils - 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 15:07:47	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:47.507 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:47.546 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:47.546 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:47.546 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:47.554 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:47.555 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:47.555 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:47.555 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:47.556 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:47.702 INFO  Funcotator - Initializing Funcotator Engine...
15:07:47.702 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:07:47.702 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.
15:07:47.702 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator1193534456542339484.vcf
15:07:47.706 INFO  ProgressMeter - Starting traversal
15:07:47.706 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:53.008 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
15:07:53.008 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
15:07:53.009 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          17050.7
15:07:53.009 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
15:07:53.009 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
15:07:53.033 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:53 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3019898880
15:07:53.033 WARN  gatk -   VCF Elapsed Time: 6.280366763s
15:07:53.034 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/regressionTestHg19Large.vcf.funcotator1193534456542339484.vcf
15:07:53.042 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large_expected.vcf
15:07:53.174 INFO  Funcotator - ------------------------------------------------------------
15:07:53.174 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:53.174 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:53.174 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:53.174 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:53.174 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:53 PM GMT
15:07:53.174 INFO  Funcotator - ------------------------------------------------------------
15:07:53.174 INFO  Funcotator - ------------------------------------------------------------
15:07:53.174 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:53.174 INFO  Funcotator - Picard Version: 3.4.0
15:07:53.174 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:53.174 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:53.174 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:53.174 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:53.174 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:53.174 INFO  Funcotator - Deflater: IntelDeflater
15:07:53.174 INFO  Funcotator - Inflater: IntelInflater
15:07:53.174 INFO  Funcotator - GCS max retries/reopens: 20
15:07:53.174 INFO  Funcotator - Requester pays: disabled
15:07:53.174 INFO  Funcotator - Initializing engine
15:07:53.176 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestHg19Large.vcf
15:07:53.178 INFO  Funcotator - Done initializing engine
15:07:53.178 INFO  Funcotator - Validating sequence dictionaries...
15:07:53.178 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:53.178 INFO  Funcotator - Initializing data sources...
15:07:53.178 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:53.178 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:53.178 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:53.179 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:53.179 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:53.179 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:53.179 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:53.179 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:53.180 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:53.180 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:53.180 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:53.180 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:53.180 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:53.180 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:53.181 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:53.181 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:53.181 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:53.181 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:53.181 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:53.181 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:53.202 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:53.203 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:53.248 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:53.249 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:53.795 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:53.795 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:53.796 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:53.798 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:53.800 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:53.802 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:53.803 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:53.803 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:53.830 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:53.830 INFO  DataSourceUtils - 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 15:07:53	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:53.831 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:53.869 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:53.870 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:53.870 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:53.877 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:53.878 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:53.878 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:53.879 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:53.879 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:54.041 INFO  Funcotator - Initializing Funcotator Engine...
15:07:54.041 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:07:54.041 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.
15:07:54.041 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestHg19Large.vcf.funcotator15034958485574943434.maf
15:07:54.041 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
15:07:54.042 INFO  ProgressMeter - Starting traversal
15:07:54.042 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:07:59.047 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, ref allele: G)
15:07:59.047 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=956, alt allele: A)
15:07:59.048 INFO  ProgressMeter -        chr1:46543210              0.1                  1507          18062.3
15:07:59.048 INFO  ProgressMeter - Traversal complete. Processed 1507 total variants in 0.1 minutes.
15:07:59.048 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/398
15:07:59.049 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:07:59 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3019898880
15:07:59.049 WARN  gatk -   MAF Elapsed Time: 5.985766893s
15:07:59.162 INFO  Funcotator - ------------------------------------------------------------
15:07:59.162 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:07:59.162 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:59.162 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:07:59.162 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:07:59.162 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:07:59 PM GMT
15:07:59.162 INFO  Funcotator - ------------------------------------------------------------
15:07:59.162 INFO  Funcotator - ------------------------------------------------------------
15:07:59.162 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:07:59.162 INFO  Funcotator - Picard Version: 3.4.0
15:07:59.162 INFO  Funcotator - Built for Spark Version: 3.5.0
15:07:59.162 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:59.162 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:59.162 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:59.162 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:59.162 INFO  Funcotator - Deflater: IntelDeflater
15:07:59.162 INFO  Funcotator - Inflater: IntelInflater
15:07:59.162 INFO  Funcotator - GCS max retries/reopens: 20
15:07:59.162 INFO  Funcotator - Requester pays: disabled
15:07:59.162 INFO  Funcotator - Initializing engine
15:07:59.165 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
15:07:59.166 INFO  Funcotator - Done initializing engine
15:07:59.166 INFO  Funcotator - Validating sequence dictionaries...
15:07:59.166 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:07:59.166 INFO  Funcotator - Initializing data sources...
15:07:59.166 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:07:59.166 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:07:59.167 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:59.167 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:59.167 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:59.167 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:59.167 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:59.168 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:59.168 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:59.168 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:59.168 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:07:59.168 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:59.169 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:59.169 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:59.169 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:59.169 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:59.169 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:59.169 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:07:59.169 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:07:59.170 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:07:59.190 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:07:59.191 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:07:59.237 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:07:59.238 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:07:59.817 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:59.818 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:07:59.819 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:59.820 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:59.823 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:07:59.825 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:07:59.825 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:59.826 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:07:59.863 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:07:59.863 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:07:59	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:07:59.863 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
15:07:59.903 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:07:59.903 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:07:59.903 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:07:59.911 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:07:59.911 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:59.911 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:07:59.912 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:07:59.913 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:07:59.994 INFO  Funcotator - Initializing Funcotator Engine...
15:07:59.994 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:07:59.994 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.
15:07:59.994 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator1652436146575391959.vcf
15:07:59.995 INFO  ProgressMeter - Starting traversal
15:07:59.995 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:01.942 INFO  ProgressMeter -             unmapped              0.0                   198           6101.7
15:08:01.942 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:08:01.942 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:08:01.953 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:01 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3019898880
15:08:02.050 INFO  Funcotator - ------------------------------------------------------------
15:08:02.050 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:02.050 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:02.050 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:02.050 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:02.050 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:02 PM GMT
15:08:02.050 INFO  Funcotator - ------------------------------------------------------------
15:08:02.050 INFO  Funcotator - ------------------------------------------------------------
15:08:02.050 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:02.050 INFO  Funcotator - Picard Version: 3.4.0
15:08:02.050 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:02.050 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:02.051 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:02.051 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:02.051 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:02.051 INFO  Funcotator - Deflater: IntelDeflater
15:08:02.051 INFO  Funcotator - Inflater: IntelInflater
15:08:02.051 INFO  Funcotator - GCS max retries/reopens: 20
15:08:02.051 INFO  Funcotator - Requester pays: disabled
15:08:02.051 INFO  Funcotator - Initializing engine
15:08:02.054 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
15:08:02.055 INFO  Funcotator - Done initializing engine
15:08:02.056 INFO  Funcotator - Validating sequence dictionaries...
15:08:02.056 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:02.056 INFO  Funcotator - Initializing data sources...
15:08:02.056 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:02.056 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:02.056 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:02.056 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:02.057 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:02.057 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:02.057 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:02.057 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:02.057 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:02.057 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:02.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:02.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:02.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:02.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:02.058 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:02.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:02.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:02.059 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:02.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:02.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:02.081 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:02.082 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:02.130 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:02.131 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:02.724 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
15:08:02.724 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:02.725 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:02.727 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
15:08:02.730 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:02.732 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:02.733 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:02.733 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:02.761 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:02.761 INFO  DataSourceUtils - 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 15:08:02	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:02.761 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:02.801 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:02.801 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:02.801 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:02.810 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:02.810 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:02.810 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:02.811 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:02.811 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:02.951 INFO  Funcotator - Initializing Funcotator Engine...
15:08:02.952 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:08:02.952 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.
15:08:02.952 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1_expected.vcf.funcotator15940666309336557685.maf
15:08:02.952 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
15:08:02.953 INFO  ProgressMeter - Starting traversal
15:08:02.953 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:04.800 INFO  ProgressMeter -             unmapped              0.0                   198           6432.1
15:08:04.800 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:08:04.800 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:08:04.800 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:04 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3019898880
15:08:04.894 INFO  Funcotator - ------------------------------------------------------------
15:08:04.894 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:04.894 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:04.894 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:04.894 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:04.894 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:04 PM GMT
15:08:04.894 INFO  Funcotator - ------------------------------------------------------------
15:08:04.895 INFO  Funcotator - ------------------------------------------------------------
15:08:04.895 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:04.895 INFO  Funcotator - Picard Version: 3.4.0
15:08:04.895 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:04.895 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:04.895 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:04.895 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:04.895 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:04.895 INFO  Funcotator - Deflater: IntelDeflater
15:08:04.895 INFO  Funcotator - Inflater: IntelInflater
15:08:04.895 INFO  Funcotator - GCS max retries/reopens: 20
15:08:04.895 INFO  Funcotator - Requester pays: disabled
15:08:04.895 INFO  Funcotator - Initializing engine
15:08:04.897 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1_expected.vcf
15:08:04.898 INFO  Funcotator - Done initializing engine
15:08:04.898 INFO  Funcotator - Validating sequence dictionaries...
15:08:04.899 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:04.899 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:04 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3019898880
15:08:04.992 INFO  Funcotator - ------------------------------------------------------------
15:08:04.992 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:04.992 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:04.992 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:04.992 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:04.992 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:04 PM GMT
15:08:04.992 INFO  Funcotator - ------------------------------------------------------------
15:08:04.992 INFO  Funcotator - ------------------------------------------------------------
15:08:04.992 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:04.992 INFO  Funcotator - Picard Version: 3.4.0
15:08:04.992 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:04.992 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:04.992 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:04.992 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:04.992 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:04.992 INFO  Funcotator - Deflater: IntelDeflater
15:08:04.992 INFO  Funcotator - Inflater: IntelInflater
15:08:04.992 INFO  Funcotator - GCS max retries/reopens: 20
15:08:04.992 INFO  Funcotator - Requester pays: disabled
15:08:04.992 INFO  Funcotator - Initializing engine
15:08:04.994 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:08:05.019 INFO  Funcotator - Done initializing engine
15:08:05.019 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:05.019 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:05.019 INFO  Funcotator - Initializing data sources...
15:08:05.019 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:05.019 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:05.019 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
15:08:05.019 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
15:08:05.019 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
15:08:05.019 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:05.019 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
15:08:05.019 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:05.020 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
15:08:05.020 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
15:08:05.021 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
15:08:05.021 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:05.022 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
15:08:05.031 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
15:08:05.040 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
15:08:05.048 INFO  Funcotator - Initializing Funcotator Engine...
15:08:05.052 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:05.052 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out16795772614324072514.vcf
15:08:05.064 INFO  ProgressMeter - Starting traversal
15:08:05.064 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:05.091 INFO  ProgressMeter -             unmapped              0.0                   100         222222.2
15:08:05.091 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:08:05.091 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:08:05.097 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3019898880
15:08:05.098 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out16795772614324072514.vcf
15:08:05.201 INFO  Funcotator - ------------------------------------------------------------
15:08:05.201 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:05.201 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:05.201 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:05.201 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:05.201 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:05 PM GMT
15:08:05.201 INFO  Funcotator - ------------------------------------------------------------
15:08:05.201 INFO  Funcotator - ------------------------------------------------------------
15:08:05.201 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:05.201 INFO  Funcotator - Picard Version: 3.4.0
15:08:05.201 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:05.202 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:05.202 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:05.202 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:05.202 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:05.202 INFO  Funcotator - Deflater: IntelDeflater
15:08:05.202 INFO  Funcotator - Inflater: IntelInflater
15:08:05.202 INFO  Funcotator - GCS max retries/reopens: 20
15:08:05.202 INFO  Funcotator - Requester pays: disabled
15:08:05.202 INFO  Funcotator - Initializing engine
15:08:05.203 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:08:05.205 INFO  Funcotator - Done initializing engine
15:08:05.205 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:05.205 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:05.205 INFO  Funcotator - Initializing data sources...
15:08:05.205 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:05.205 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:05.205 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
15:08:05.205 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
15:08:05.206 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
15:08:05.206 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:05.206 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
15:08:05.206 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:05.207 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
15:08:05.207 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
15:08:05.207 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
15:08:05.207 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:05.208 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
15:08:05.209 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
15:08:05.211 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
15:08:05.211 INFO  Funcotator - Initializing Funcotator Engine...
15:08:05.212 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:05.212 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.
15:08:05.212 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4480524523959903193.vcf
15:08:05.215 INFO  ProgressMeter - Starting traversal
15:08:05.215 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:05.224 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
15:08:05.224 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:08:05.224 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:08:05.226 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3019898880
15:08:05.227 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4480524523959903193.vcf
15:08:05.321 INFO  Funcotator - ------------------------------------------------------------
15:08:05.321 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:05.321 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:05.321 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:05.321 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:05.321 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:05 PM GMT
15:08:05.321 INFO  Funcotator - ------------------------------------------------------------
15:08:05.321 INFO  Funcotator - ------------------------------------------------------------
15:08:05.322 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:05.322 INFO  Funcotator - Picard Version: 3.4.0
15:08:05.322 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:05.322 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:05.322 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:05.322 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:05.322 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:05.322 INFO  Funcotator - Deflater: IntelDeflater
15:08:05.322 INFO  Funcotator - Inflater: IntelInflater
15:08:05.322 INFO  Funcotator - GCS max retries/reopens: 20
15:08:05.322 INFO  Funcotator - Requester pays: disabled
15:08:05.322 INFO  Funcotator - Initializing engine
15:08:05.323 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
15:08:05.336 INFO  Funcotator - Done initializing engine
15:08:05.336 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:05.336 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:05.336 INFO  Funcotator - Initializing data sources...
15:08:05.336 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:05.336 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:05.336 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
15:08:05.336 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
15:08:05.337 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
15:08:05.337 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:05.337 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
15:08:05.337 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:05.337 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
15:08:05.338 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
15:08:05.338 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
15:08:05.338 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:05.339 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
15:08:05.347 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
15:08:05.355 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
15:08:05.375 INFO  Funcotator - Initializing Funcotator Engine...
15:08:05.379 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:05.379 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out15847136167783094836.vcf
15:08:05.389 INFO  ProgressMeter - Starting traversal
15:08:05.389 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:05.394 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)
15:08:05.394 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)
15:08:05.394 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:05.394 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:08:05.394 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:08:05.395 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:08:05.397 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:05.397 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:08:05.397 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:08:05.397 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:08:05.398 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)
15:08:05.398 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)
15:08:05.398 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:05.398 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:08:05.398 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:08:05.398 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:08:05.399 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)
15:08:05.399 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)
15:08:05.399 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
15:08:05.399 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
15:08:05.400 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:08:05.400 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:08:05.400 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:05.400 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:08:05.401 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:08:05.401 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:08:05.401 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:05.402 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:08:05.402 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:08:05.402 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:08:05.402 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)
15:08:05.403 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)
15:08:05.403 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:08:05.403 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:08:05.403 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:08:05.403 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:08:05.403 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)
15:08:05.404 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)
15:08:05.404 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:05.404 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:08:05.404 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:08:05.404 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:08:05.405 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:08:05.405 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:08:05.405 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:08:05.405 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:08:05.406 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)
15:08:05.406 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)
15:08:05.406 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:05.406 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:08:05.406 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:08:05.406 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:08:05.407 INFO  ProgressMeter -             unmapped              0.0                    10          33333.3
15:08:05.407 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
15:08:05.407 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:08:05.412 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:05 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3019898880
15:08:05.413 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out15847136167783094836.vcf
15:08:05.511 INFO  Funcotator - ------------------------------------------------------------
15:08:05.511 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:05.511 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:05.511 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:05.511 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:05.511 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:05 PM GMT
15:08:05.511 INFO  Funcotator - ------------------------------------------------------------
15:08:05.511 INFO  Funcotator - ------------------------------------------------------------
15:08:05.511 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:05.511 INFO  Funcotator - Picard Version: 3.4.0
15:08:05.511 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:05.511 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:05.511 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:05.511 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:05.511 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:05.511 INFO  Funcotator - Deflater: IntelDeflater
15:08:05.511 INFO  Funcotator - Inflater: IntelInflater
15:08:05.511 INFO  Funcotator - GCS max retries/reopens: 20
15:08:05.511 INFO  Funcotator - Requester pays: disabled
15:08:05.511 INFO  Funcotator - Initializing engine
15:08:05.513 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/non_locatable_proof_input.vcf
15:08:05.515 INFO  Funcotator - Done initializing engine
15:08:05.515 INFO  Funcotator - Validating sequence dictionaries...
15:08:05.515 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:05.515 INFO  Funcotator - Initializing data sources...
15:08:05.515 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:05.515 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:05.515 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:05.515 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:05.515 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:05.516 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:05.516 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:05.516 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:05.516 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:05.516 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:05.517 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:05.517 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:05.517 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:05.517 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:05.517 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:05.518 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:05.518 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:05.518 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:05.518 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:05.518 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:05.540 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:05.540 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:05.586 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:05.586 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:06.216 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
15:08:06.216 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:06.217 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:06.219 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:06.221 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:06.223 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:06.224 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:06.224 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:06.252 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:06.252 INFO  DataSourceUtils - 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 15:08:06	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:06.253 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:06.290 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:06.291 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
15:08:06.291 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
15:08:06.298 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:06.299 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:06.299 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:06.300 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:06.300 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:06.383 INFO  Funcotator - Initializing Funcotator Engine...
15:08:06.383 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:08:06.383 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.
15:08:06.383 INFO  Funcotator - Creating a VCF file for output: file:/tmp/non_locatable_proof_input.vcf.funcotator2496337034633298266.vcf
15:08:06.387 INFO  ProgressMeter - Starting traversal
15:08:06.387 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:06.432 INFO  ProgressMeter -             unmapped              0.0                     1           1333.3
15:08:06.433 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:08:06.433 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:08:06.433 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:06 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3061841920
15:08:06.434 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/non_locatable_proof_input.vcf.funcotator2496337034633298266.vcf
15:08:06.595 INFO  Funcotator - ------------------------------------------------------------
15:08:06.595 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:06.595 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:06.595 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:06.595 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:06.595 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:06 PM GMT
15:08:06.595 INFO  Funcotator - ------------------------------------------------------------
15:08:06.595 INFO  Funcotator - ------------------------------------------------------------
15:08:06.595 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:06.595 INFO  Funcotator - Picard Version: 3.4.0
15:08:06.595 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:06.595 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:06.595 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:06.595 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:06.595 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:06.595 INFO  Funcotator - Deflater: IntelDeflater
15:08:06.595 INFO  Funcotator - Inflater: IntelInflater
15:08:06.595 INFO  Funcotator - GCS max retries/reopens: 20
15:08:06.595 INFO  Funcotator - Requester pays: disabled
15:08:06.595 INFO  Funcotator - Initializing engine
15:08:06.598 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/symbollic_allele_proof_input.vcf
15:08:06.599 INFO  Funcotator - Done initializing engine
15:08:06.599 INFO  Funcotator - Validating sequence dictionaries...
15:08:06.599 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:06.599 INFO  Funcotator - Initializing data sources...
15:08:06.599 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:06.599 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:06.600 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:06.600 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:06.600 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:06.600 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:06.600 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:06.601 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:06.601 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:06.601 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:06.601 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:06.601 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:06.601 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:06.602 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:06.602 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:06.602 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:06.602 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:06.602 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:06.602 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:06.602 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:06.622 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:06.623 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:06.669 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:06.670 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:07.345 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:07.345 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:07.346 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:07.348 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:07.351 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:07.353 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:07.353 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:07.354 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:07.381 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:07.381 INFO  DataSourceUtils - 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 15:08:07	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:07.381 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:07.445 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:07.445 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:07.446 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:07.453 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:07.453 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:07.453 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:07.454 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:07.455 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:07.535 INFO  Funcotator - Initializing Funcotator Engine...
15:08:07.535 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:08:07.535 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.
15:08:07.535 INFO  Funcotator - Creating a VCF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator12537591972733310010.vcf
15:08:07.539 INFO  ProgressMeter - Starting traversal
15:08:07.539 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:07.546 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1007545-1007545 due to alternate allele: <NON_REF>
15:08:07.582 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:08:07.582 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:08:07.582 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:08:07.582 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:08:07.582 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:08:07.582 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:08:07.582 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1335002-1335002 due to alternate allele: <NON_REF>
15:08:07.585 INFO  ProgressMeter -             unmapped              0.0                     2           2608.7
15:08:07.585 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:08:07.585 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:08:07.586 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:07 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=3164602368
15:08:07.586 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/symbollic_allele_proof_input.vcf.funcotator12537591972733310010.vcf
15:08:07.700 INFO  Funcotator - ------------------------------------------------------------
15:08:07.700 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:07.700 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:07.700 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:07.700 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:07.700 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:07 PM GMT
15:08:07.700 INFO  Funcotator - ------------------------------------------------------------
15:08:07.700 INFO  Funcotator - ------------------------------------------------------------
15:08:07.700 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:07.700 INFO  Funcotator - Picard Version: 3.4.0
15:08:07.700 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:07.700 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:07.700 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:07.700 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:07.700 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:07.700 INFO  Funcotator - Deflater: IntelDeflater
15:08:07.700 INFO  Funcotator - Inflater: IntelInflater
15:08:07.700 INFO  Funcotator - GCS max retries/reopens: 20
15:08:07.700 INFO  Funcotator - Requester pays: disabled
15:08:07.700 INFO  Funcotator - Initializing engine
15:08:07.702 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/custom_vc_order_files/custom_vc_input_test.vcf
15:08:07.704 INFO  Funcotator - Done initializing engine
15:08:07.704 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:07.704 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:07.704 INFO  Funcotator - Initializing data sources...
15:08:07.704 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:07.704 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:07.704 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:07.704 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:07.704 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:07.705 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:07.705 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:07.705 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:07.705 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:07.705 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:07.705 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:07.706 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:07.706 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:07.706 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:07.706 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:07.707 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:07.707 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:07.707 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:07.707 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:07.707 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:07.727 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:07.728 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:07.773 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:07.774 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:08.457 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:08.457 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:08.458 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:08.460 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:08.463 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:08.465 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:08.465 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:08.466 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:08.493 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:08.493 INFO  DataSourceUtils - 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 15:08:08	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:08.493 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:08.531 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:08.531 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:08.531 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:08.539 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:08.539 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:08.539 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:08.540 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:08.540 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:08.624 INFO  Funcotator - Initializing Funcotator Engine...
15:08:08.624 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:08.624 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.
15:08:08.624 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
15:08:08.625 INFO  FuncotatorUtils -     Setting new Variant Classification severity: INTRON = 0
15:08:08.625 INFO  FuncotatorUtils -     Setting new Variant Classification severity: SILENT = 999
15:08:08.625 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out16661819675940822539.vcf
15:08:08.628 INFO  ProgressMeter - Starting traversal
15:08:08.628 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:08.660 INFO  ProgressMeter -             unmapped              0.0                     1           1875.0
15:08:08.660 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:08:08.660 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:08:08.661 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:08 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2174746624
15:08:08.662 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out16661819675940822539.vcf
15:08:08.663 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 3:08:08 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2174746624
[May 27, 2025 at 3:08:08 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2174746624
15:08:08.994 INFO  Funcotator - ------------------------------------------------------------
15:08:08.994 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:08.994 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:08.994 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:08.994 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:08.994 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:08 PM GMT
15:08:08.994 INFO  Funcotator - ------------------------------------------------------------
15:08:08.994 INFO  Funcotator - ------------------------------------------------------------
15:08:08.994 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:08.994 INFO  Funcotator - Picard Version: 3.4.0
15:08:08.994 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:08.994 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:08.994 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:08.994 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:08.994 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:08.994 INFO  Funcotator - Deflater: IntelDeflater
15:08:08.994 INFO  Funcotator - Inflater: IntelInflater
15:08:08.994 INFO  Funcotator - GCS max retries/reopens: 20
15:08:08.994 INFO  Funcotator - Requester pays: disabled
15:08:08.994 INFO  Funcotator - Initializing engine
15:08:08.995 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:08:09.012 INFO  Funcotator - Done initializing engine
15:08:09.012 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:09.012 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:09.012 INFO  Funcotator - Initializing data sources...
15:08:09.012 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:09.012 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:09.012 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
15:08:09.012 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
15:08:09.013 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
15:08:09.013 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:09.013 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
15:08:09.013 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:09.013 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
15:08:09.014 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
15:08:09.014 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
15:08:09.014 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:09.015 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
15:08:09.023 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
15:08:09.031 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
15:08:09.039 INFO  Funcotator - Initializing Funcotator Engine...
15:08:09.046 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:09.046 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4905307822900866918.vcf
15:08:09.059 INFO  ProgressMeter - Starting traversal
15:08:09.059 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:09.134 INFO  ProgressMeter -             unmapped              0.0                   100          80000.0
15:08:09.134 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:08:09.134 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:08:09.141 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:09 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2174746624
15:08:09.142 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4905307822900866918.vcf
15:08:09.259 INFO  Funcotator - ------------------------------------------------------------
15:08:09.259 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:09.259 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:09.259 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:09.259 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:09.259 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:09 PM GMT
15:08:09.259 INFO  Funcotator - ------------------------------------------------------------
15:08:09.259 INFO  Funcotator - ------------------------------------------------------------
15:08:09.259 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:09.259 INFO  Funcotator - Picard Version: 3.4.0
15:08:09.259 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:09.259 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:09.259 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:09.259 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:09.259 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:09.259 INFO  Funcotator - Deflater: IntelDeflater
15:08:09.259 INFO  Funcotator - Inflater: IntelInflater
15:08:09.259 INFO  Funcotator - GCS max retries/reopens: 20
15:08:09.259 INFO  Funcotator - Requester pays: disabled
15:08:09.259 INFO  Funcotator - Initializing engine
15:08:09.262 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/FILTER_test.vcf
15:08:09.263 INFO  Funcotator - Done initializing engine
15:08:09.263 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:09.263 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:09.263 INFO  Funcotator - Initializing data sources...
15:08:09.263 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_FILTER_test/
15:08:09.263 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:09.263 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
15:08:09.263 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
15:08:09.263 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
15:08:09.263 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:09.263 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
15:08:09.263 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
15:08:09.264 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
15:08:09.267 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
15:08:09.269 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
15:08:09.272 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
15:08:09.272 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:09.273 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
15:08:09.273 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
15:08:09.273 INFO  Funcotator - Initializing Funcotator Engine...
15:08:09.273 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:09.273 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.
15:08:09.273 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:09.273 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing14156816458535228767.vcf
15:08:09.276 INFO  ProgressMeter - Starting traversal
15:08:09.276 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:09.298 INFO  ProgressMeter -             unmapped              0.0                     1           2727.3
15:08:09.298 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:08:09.298 INFO  VcfFuncotationFactory - dbSnp 9606_b150 cache hits/total: 0/1
15:08:09.300 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:09 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2174746624
15:08:09.301 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing14156816458535228767.vcf
15:08:09.393 INFO  Funcotator - ------------------------------------------------------------
15:08:09.393 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:09.393 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:09.393 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:09.393 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:09.393 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:09 PM GMT
15:08:09.393 INFO  Funcotator - ------------------------------------------------------------
15:08:09.393 INFO  Funcotator - ------------------------------------------------------------
15:08:09.393 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:09.393 INFO  Funcotator - Picard Version: 3.4.0
15:08:09.393 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:09.393 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:09.393 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:09.393 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:09.393 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:09.393 INFO  Funcotator - Deflater: IntelDeflater
15:08:09.393 INFO  Funcotator - Inflater: IntelInflater
15:08:09.394 INFO  Funcotator - GCS max retries/reopens: 20
15:08:09.394 INFO  Funcotator - Requester pays: disabled
15:08:09.394 INFO  Funcotator - Initializing engine
15:08:09.394 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:08:09.395 INFO  Funcotator - Done initializing engine
15:08:09.395 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:09.395 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:09.395 INFO  Funcotator - Initializing data sources...
15:08:09.395 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:09.395 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:09.396 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
15:08:09.396 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
15:08:09.396 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:09.396 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:09.396 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:09.396 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:09.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:09.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:09.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:09.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:09.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:09.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:09.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:09.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:09.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:09.398 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:09.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:09.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:09.419 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:09.419 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:09.466 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:09.467 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:10.076 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:10.076 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:10.077 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:10.079 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
15:08:10.081 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:10.083 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:10.084 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:10.084 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:10.111 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:10.111 INFO  DataSourceUtils - 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 15:08:10	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:10.112 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:10.149 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:10.149 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:10.150 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:10.157 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:10.158 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:10.158 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:10.158 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:10.159 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:10.239 INFO  Funcotator - Initializing Funcotator Engine...
15:08:10.239 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
15:08:10.240 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:08:10.240 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:08:10.240 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:08:10.240 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:08:10.240 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:10.240 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out821265852736866975.vcf
15:08:10.241 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
15:08:10.242 INFO  ProgressMeter - Starting traversal
15:08:10.242 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:10.261 INFO  ProgressMeter -             unmapped              0.0                     3           9473.7
15:08:10.261 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:08:10.261 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:08:10.263 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:10 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2174746624
15:08:10.351 INFO  Funcotator - ------------------------------------------------------------
15:08:10.351 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:10.351 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:10.351 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:10.351 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:10.351 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:10 PM GMT
15:08:10.351 INFO  Funcotator - ------------------------------------------------------------
15:08:10.351 INFO  Funcotator - ------------------------------------------------------------
15:08:10.351 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:10.351 INFO  Funcotator - Picard Version: 3.4.0
15:08:10.351 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:10.351 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:10.351 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:10.351 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:10.351 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:10.352 INFO  Funcotator - Deflater: IntelDeflater
15:08:10.352 INFO  Funcotator - Inflater: IntelInflater
15:08:10.352 INFO  Funcotator - GCS max retries/reopens: 20
15:08:10.352 INFO  Funcotator - Requester pays: disabled
15:08:10.352 INFO  Funcotator - Initializing engine
15:08:10.352 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:08:10.353 INFO  Funcotator - Done initializing engine
15:08:10.353 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:10.353 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:10.353 INFO  Funcotator - Initializing data sources...
15:08:10.353 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:10.353 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:10.353 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:10.354 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:10.354 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:10.354 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:10.354 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:10.354 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:10.355 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:10.355 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:10.355 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:10.355 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:10.355 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:10.355 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:10.356 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:10.356 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:10.356 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:10.356 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:10.356 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:10.356 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:10.377 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:10.377 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:10.424 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:10.424 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:11.007 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:11.007 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:11.009 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:11.011 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:11.014 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:11.016 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:11.016 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:11.017 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:11.044 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:11.044 INFO  DataSourceUtils - 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 15:08:11	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:11.044 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:11.082 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:11.082 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:11.082 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:11.090 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:11.091 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:11.091 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:11.092 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:11.092 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:11.172 INFO  Funcotator - Initializing Funcotator Engine...
15:08:11.172 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:11.172 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:11.172 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12164594704664206321.vcf
15:08:11.173 INFO  ProgressMeter - Starting traversal
15:08:11.173 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:11.272 INFO  ProgressMeter -             unmapped              0.0                     4           2424.2
15:08:11.272 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:08:11.272 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:08:11.273 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:11 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2174746624
15:08:11.373 INFO  Funcotator - ------------------------------------------------------------
15:08:11.373 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:11.373 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:11.373 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:11.373 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:11.373 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:11 PM GMT
15:08:11.373 INFO  Funcotator - ------------------------------------------------------------
15:08:11.373 INFO  Funcotator - ------------------------------------------------------------
15:08:11.373 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:11.373 INFO  Funcotator - Picard Version: 3.4.0
15:08:11.373 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:11.373 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:11.373 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:11.373 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:11.373 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:11.373 INFO  Funcotator - Deflater: IntelDeflater
15:08:11.373 INFO  Funcotator - Inflater: IntelInflater
15:08:11.373 INFO  Funcotator - GCS max retries/reopens: 20
15:08:11.373 INFO  Funcotator - Requester pays: disabled
15:08:11.373 INFO  Funcotator - Initializing engine
15:08:11.374 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:08:11.374 INFO  Funcotator - Done initializing engine
15:08:11.375 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:11.375 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:11.375 INFO  Funcotator - Initializing data sources...
15:08:11.375 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:11.375 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:11.375 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:11.375 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:11.375 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:11.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:11.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:11.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:11.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:11.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:11.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:11.376 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:11.377 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:11.377 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:11.377 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:11.377 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:11.377 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:11.377 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:11.377 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:11.378 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
15:08:11.402 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:11.402 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:11.449 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:11.449 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:12.037 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:12.037 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:12.038 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:12.040 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:12.043 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:12.045 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:12.045 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:12.046 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:12.073 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:12.073 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:08:12	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:12.074 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:12.112 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:12.113 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:12.113 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:12.120 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:12.121 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:12.121 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:12.122 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:12.122 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:12.204 INFO  Funcotator - Initializing Funcotator Engine...
15:08:12.204 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
15:08:12.205 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:08:12.205 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:08:12.205 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:08:12.205 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:08:12.206 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:08:12.206 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:08:12.206 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:08:12.206 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:12.206 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out9814525609671908160.vcf
15:08:12.206 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
15:08:12.207 INFO  ProgressMeter - Starting traversal
15:08:12.207 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:12.227 INFO  ProgressMeter -             unmapped              0.0                     3           9000.0
15:08:12.227 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:08:12.227 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:08:12.229 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:12 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2174746624
15:08:12.326 INFO  Funcotator - ------------------------------------------------------------
15:08:12.326 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:12.326 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:12.326 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:12.326 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:12.326 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:12 PM GMT
15:08:12.326 INFO  Funcotator - ------------------------------------------------------------
15:08:12.326 INFO  Funcotator - ------------------------------------------------------------
15:08:12.326 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:12.326 INFO  Funcotator - Picard Version: 3.4.0
15:08:12.326 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:12.326 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:12.326 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:12.326 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:12.326 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:12.326 INFO  Funcotator - Deflater: IntelDeflater
15:08:12.326 INFO  Funcotator - Inflater: IntelInflater
15:08:12.326 INFO  Funcotator - GCS max retries/reopens: 20
15:08:12.326 INFO  Funcotator - Requester pays: disabled
15:08:12.326 INFO  Funcotator - Initializing engine
15:08:12.327 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:08:12.328 INFO  Funcotator - Done initializing engine
15:08:12.328 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:12.328 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:12.328 INFO  Funcotator - Initializing data sources...
15:08:12.328 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:12.328 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:12.328 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:12.329 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:12.329 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:12.329 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:12.329 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:12.329 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:12.330 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:12.330 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
15:08:12.330 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:12.330 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:12.330 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:12.330 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:12.331 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:12.331 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:12.331 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
15:08:12.331 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:12.331 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:12.331 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:12.357 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:12.357 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
15:08:12.402 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
15:08:12.403 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:12.990 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:12.990 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:12.991 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:12.993 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:12.995 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:12.997 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:12.998 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:12.998 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:13.025 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:13.025 INFO  DataSourceUtils - 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 15:08:13	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:13.025 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:13.115 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:13.115 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:13.115 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:13.122 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:13.123 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:13.123 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:13.124 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:13.124 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:13.204 INFO  Funcotator - Initializing Funcotator Engine...
15:08:13.204 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:13.204 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:13.204 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out2780816676997083796.vcf
15:08:13.206 INFO  ProgressMeter - Starting traversal
15:08:13.206 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:13.302 INFO  ProgressMeter -             unmapped              0.0                     4           2500.0
15:08:13.303 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:08:13.303 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:08:13.303 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:13 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2174746624
15:08:13.394 INFO  Funcotator - ------------------------------------------------------------
15:08:13.394 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:13.394 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:13.394 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:13.394 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:13.394 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:13 PM GMT
15:08:13.394 INFO  Funcotator - ------------------------------------------------------------
15:08:13.394 INFO  Funcotator - ------------------------------------------------------------
15:08:13.394 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:13.394 INFO  Funcotator - Picard Version: 3.4.0
15:08:13.394 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:13.394 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:13.394 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:13.394 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:13.394 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:13.394 INFO  Funcotator - Deflater: IntelDeflater
15:08:13.394 INFO  Funcotator - Inflater: IntelInflater
15:08:13.394 INFO  Funcotator - GCS max retries/reopens: 20
15:08:13.394 INFO  Funcotator - Requester pays: disabled
15:08:13.394 INFO  Funcotator - Initializing engine
15:08:13.395 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:08:13.396 INFO  Funcotator - Done initializing engine
15:08:13.396 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:13.396 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:13.396 INFO  Funcotator - Initializing data sources...
15:08:13.396 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:13.396 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:13.396 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
15:08:13.396 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
15:08:13.396 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:13.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:13.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:13.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:13.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:13.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:13.397 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:13.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:13.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:13.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:13.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:13.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:13.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:13.398 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:13.398 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:13.399 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:13.419 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:13.419 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:13.466 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:13.466 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:14.138 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:14.138 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:14.139 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:14.141 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:14.144 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:14.147 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:14.147 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:14.148 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:14.175 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:14.175 INFO  DataSourceUtils - 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 15:08:14	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:14.175 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:14.213 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:14.213 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:14.214 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:14.221 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:14.221 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:14.221 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:14.222 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:14.222 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:14.303 INFO  Funcotator - Initializing Funcotator Engine...
15:08:14.303 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
15:08:14.303 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:08:14.303 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:08:14.303 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:08:14.303 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:08:14.303 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:08:14.303 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:08:14.303 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:08:14.303 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:08:14.303 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:08:14.303 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:08:14.304 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:08:14.304 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:14.304 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6171698895622084705.maf
15:08:14.305 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
15:08:14.305 INFO  ProgressMeter - Starting traversal
15:08:14.305 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:14.324 INFO  ProgressMeter -             unmapped              0.0                     3           9473.7
15:08:14.324 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:08:14.324 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:08:14.324 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:14 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2287992832
15:08:14.424 INFO  Funcotator - ------------------------------------------------------------
15:08:14.424 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:14.424 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:14.424 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:14.424 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:14.424 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:14 PM GMT
15:08:14.424 INFO  Funcotator - ------------------------------------------------------------
15:08:14.424 INFO  Funcotator - ------------------------------------------------------------
15:08:14.425 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:14.425 INFO  Funcotator - Picard Version: 3.4.0
15:08:14.425 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:14.425 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:14.425 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:14.425 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:14.425 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:14.425 INFO  Funcotator - Deflater: IntelDeflater
15:08:14.425 INFO  Funcotator - Inflater: IntelInflater
15:08:14.425 INFO  Funcotator - GCS max retries/reopens: 20
15:08:14.425 INFO  Funcotator - Requester pays: disabled
15:08:14.425 INFO  Funcotator - Initializing engine
15:08:14.426 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:08:14.426 INFO  Funcotator - Done initializing engine
15:08:14.426 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:14.426 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:14.426 INFO  Funcotator - Initializing data sources...
15:08:14.426 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:14.426 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:14.427 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:14.427 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:14.427 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:14.427 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:14.427 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:14.428 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:14.428 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:14.428 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
15:08:14.428 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:14.428 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:14.428 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:14.429 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:14.429 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:14.429 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:14.429 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
15:08:14.429 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:14.429 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:14.430 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:14.451 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:14.452 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:14.500 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:14.501 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:15.163 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:15.163 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:15.164 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:15.166 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:15.169 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:15.171 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:15.172 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:15.172 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:15.200 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:15.200 INFO  DataSourceUtils - 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 15:08:15	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:15.200 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:15.267 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:15.268 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:15.268 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:15.275 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:15.276 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:15.276 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:15.277 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:15.277 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:15.367 INFO  Funcotator - Initializing Funcotator Engine...
15:08:15.367 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:15.367 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:15.367 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out12011719380844165432.maf
15:08:15.368 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
15:08:15.368 INFO  ProgressMeter - Starting traversal
15:08:15.368 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:15.489 INFO  ProgressMeter -             unmapped              0.0                     4           1983.5
15:08:15.489 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:08:15.489 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:08:15.489 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:15 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2441084928
15:08:15.579 INFO  Funcotator - ------------------------------------------------------------
15:08:15.579 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:15.579 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:15.579 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:15.579 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:15.579 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:15 PM GMT
15:08:15.579 INFO  Funcotator - ------------------------------------------------------------
15:08:15.579 INFO  Funcotator - ------------------------------------------------------------
15:08:15.579 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:15.579 INFO  Funcotator - Picard Version: 3.4.0
15:08:15.579 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:15.579 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:15.579 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:15.579 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:15.579 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:15.579 INFO  Funcotator - Deflater: IntelDeflater
15:08:15.579 INFO  Funcotator - Inflater: IntelInflater
15:08:15.579 INFO  Funcotator - GCS max retries/reopens: 20
15:08:15.579 INFO  Funcotator - Requester pays: disabled
15:08:15.579 INFO  Funcotator - Initializing engine
15:08:15.580 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr3_hg19.vcf
15:08:15.581 INFO  Funcotator - Done initializing engine
15:08:15.581 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:15.581 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:15.581 INFO  Funcotator - Initializing data sources...
15:08:15.581 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:15.581 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:15.581 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:15.581 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:15.582 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:15.582 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:15.582 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:15.582 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:15.582 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:15.582 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:15.582 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:15.583 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:15.583 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:15.583 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:15.583 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:15.583 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:15.583 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:15.583 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:15.583 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:15.584 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:15.605 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:15.605 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:15.720 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
15:08:15.721 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
15:08:16.372 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:16.372 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:16.373 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:16.375 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
15:08:16.378 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:16.380 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:16.381 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:16.381 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:16.409 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:16.409 INFO  DataSourceUtils - 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 15:08:16	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:16.409 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:16.447 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
15:08:16.447 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
15:08:16.447 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
15:08:16.454 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:16.455 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:16.455 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:16.456 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:16.456 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:16.541 INFO  Funcotator - Initializing Funcotator Engine...
15:08:16.541 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
15:08:16.541 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
15:08:16.542 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
15:08:16.542 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
15:08:16.542 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
15:08:16.542 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:16.542 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out18106723503546933669.maf
15:08:16.543 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
15:08:16.543 INFO  ProgressMeter - Starting traversal
15:08:16.543 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:16.574 INFO  ProgressMeter -             unmapped              0.0                     3           5806.5
15:08:16.574 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:08:16.574 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:08:16.574 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:16 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2441084928
15:08:16.719 INFO  Funcotator - ------------------------------------------------------------
15:08:16.719 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:16.719 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:16.719 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:16.719 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:16.719 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:16 PM GMT
15:08:16.719 INFO  Funcotator - ------------------------------------------------------------
15:08:16.719 INFO  Funcotator - ------------------------------------------------------------
15:08:16.719 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:16.719 INFO  Funcotator - Picard Version: 3.4.0
15:08:16.719 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:16.719 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:16.719 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:16.719 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:16.719 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:16.719 INFO  Funcotator - Deflater: IntelDeflater
15:08:16.719 INFO  Funcotator - Inflater: IntelInflater
15:08:16.719 INFO  Funcotator - GCS max retries/reopens: 20
15:08:16.719 INFO  Funcotator - Requester pays: disabled
15:08:16.719 INFO  Funcotator - Initializing engine
15:08:16.720 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/snpTest_chr19_hg19.vcf
15:08:16.721 INFO  Funcotator - Done initializing engine
15:08:16.721 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:16.721 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:16.721 INFO  Funcotator - Initializing data sources...
15:08:16.721 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:16.721 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:16.721 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
15:08:16.721 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:16.722 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
15:08:16.722 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:16.722 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:16.722 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:16.722 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:16.723 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
15:08:16.723 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
15:08:16.723 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:16.723 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:16.723 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:16.723 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:16.724 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
15:08:16.724 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
15:08:16.724 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:16.724 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
15:08:16.724 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:16.748 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
15:08:16.749 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:16.805 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:16.806 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:17.436 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:17.436 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:17.438 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:17.440 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:17.443 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:17.445 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:17.445 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:17.446 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:17.473 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:17.473 INFO  DataSourceUtils - 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 15:08:17	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:17.473 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:17.542 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:17.542 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:17.542 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:17.551 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:17.551 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:17.551 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:17.552 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:17.552 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:17.633 INFO  Funcotator - Initializing Funcotator Engine...
15:08:17.633 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:17.633 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:17.633 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out14700848330387107495.maf
15:08:17.634 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
15:08:17.634 INFO  ProgressMeter - Starting traversal
15:08:17.634 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:17.729 INFO  ProgressMeter -             unmapped              0.0                     4           2526.3
15:08:17.729 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:08:17.729 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/1
15:08:17.729 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2646605824
15:08:17.869 INFO  Funcotator - ------------------------------------------------------------
15:08:17.870 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:17.870 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:17.870 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:17.870 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:17.870 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:17 PM GMT
15:08:17.870 INFO  Funcotator - ------------------------------------------------------------
15:08:17.870 INFO  Funcotator - ------------------------------------------------------------
15:08:17.870 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:17.870 INFO  Funcotator - Picard Version: 3.4.0
15:08:17.870 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:17.870 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:17.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:17.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:17.870 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:17.870 INFO  Funcotator - Deflater: IntelDeflater
15:08:17.870 INFO  Funcotator - Inflater: IntelInflater
15:08:17.870 INFO  Funcotator - GCS max retries/reopens: 20
15:08:17.870 INFO  Funcotator - Requester pays: disabled
15:08:17.870 INFO  Funcotator - Initializing engine
15:08:17.871 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:08:17.896 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
15:08:17.896 INFO  Funcotator - Done initializing engine
15:08:17.896 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:17.896 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:17.896 INFO  Funcotator - Initializing data sources...
15:08:17.896 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
15:08:17.897 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:17.897 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
15:08:17.897 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
15:08:17.897 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
15:08:17.897 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:17.897 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
15:08:17.897 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:17.898 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
15:08:17.907 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
15:08:17.916 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
15:08:17.923 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
15:08:17.923 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:17.924 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
15:08:17.925 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
15:08:17.925 INFO  Funcotator - Initializing Funcotator Engine...
15:08:17.930 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:17.930 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out14162088682338064939.vcf
15:08:17.942 INFO  ProgressMeter - Starting traversal
15:08:17.942 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:17.955 INFO  ProgressMeter -             unmapped              0.0                    32         147692.3
15:08:17.955 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
15:08:17.955 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:08:17.962 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:17 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2761949184
15:08:18.066 INFO  Funcotator - ------------------------------------------------------------
15:08:18.066 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:18.066 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:18.066 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:18.066 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:18.066 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:18 PM GMT
15:08:18.066 INFO  Funcotator - ------------------------------------------------------------
15:08:18.066 INFO  Funcotator - ------------------------------------------------------------
15:08:18.066 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:18.066 INFO  Funcotator - Picard Version: 3.4.0
15:08:18.066 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:18.066 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:18.066 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:18.066 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:18.066 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:18.066 INFO  Funcotator - Deflater: IntelDeflater
15:08:18.066 INFO  Funcotator - Inflater: IntelInflater
15:08:18.066 INFO  Funcotator - GCS max retries/reopens: 20
15:08:18.066 INFO  Funcotator - Requester pays: disabled
15:08:18.066 INFO  Funcotator - Initializing engine
15:08:18.067 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:08:18.089 INFO  IntervalArgumentCollection - Processing 86751 bp from intervals
15:08:18.089 INFO  Funcotator - Done initializing engine
15:08:18.089 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:18.089 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:18.089 INFO  Funcotator - Initializing data sources...
15:08:18.089 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST/
15:08:18.089 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:18.089 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
15:08:18.089 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
15:08:18.089 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
15:08:18.089 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:18.089 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
15:08:18.090 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:18.090 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
15:08:18.098 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
15:08:18.130 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
15:08:18.138 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
15:08:18.138 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:18.138 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
15:08:18.139 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
15:08:18.139 INFO  Funcotator - Initializing Funcotator Engine...
15:08:18.146 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:18.146 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out4085085755953918302.vcf
15:08:18.158 INFO  ProgressMeter - Starting traversal
15:08:18.158 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:18.174 INFO  ProgressMeter -             unmapped              0.0                    32         120000.0
15:08:18.174 INFO  ProgressMeter - Traversal complete. Processed 32 total variants in 0.0 minutes.
15:08:18.174 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:08:18.179 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:18 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2761949184
15:08:18.179 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out14162088682338064939.vcf
15:08:18.189 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out4085085755953918302.vcf
15:08:18.295 INFO  Funcotator - ------------------------------------------------------------
15:08:18.295 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:18.295 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:18.295 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:18.295 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:18.295 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:18 PM GMT
15:08:18.295 INFO  Funcotator - ------------------------------------------------------------
15:08:18.295 INFO  Funcotator - ------------------------------------------------------------
15:08:18.295 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:18.295 INFO  Funcotator - Picard Version: 3.4.0
15:08:18.295 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:18.295 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:18.295 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:18.295 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:18.295 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:18.295 INFO  Funcotator - Deflater: IntelDeflater
15:08:18.295 INFO  Funcotator - Inflater: IntelInflater
15:08:18.295 INFO  Funcotator - GCS max retries/reopens: 20
15:08:18.295 INFO  Funcotator - Requester pays: disabled
15:08:18.295 INFO  Funcotator - Initializing engine
15:08:18.297 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/NotM2_test_custom_maf_fields.vcf
15:08:18.298 INFO  Funcotator - Done initializing engine
15:08:18.298 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:18.298 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:18.298 INFO  Funcotator - Initializing data sources...
15:08:18.298 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:18.298 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:18.298 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
15:08:18.298 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
15:08:18.298 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
15:08:18.298 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:18.298 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
15:08:18.298 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:18.299 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
15:08:18.299 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
15:08:18.299 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
15:08:18.299 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:18.300 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
15:08:18.301 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
15:08:18.302 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
15:08:18.303 INFO  Funcotator - Initializing Funcotator Engine...
15:08:18.303 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:18.303 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.
15:08:18.303 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out6103853392603459144.maf
15:08:18.303 INFO  ProgressMeter - Starting traversal
15:08:18.303 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:18.305 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 @ 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
15:08:18.306 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 @ 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
15:08:18.306 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 @ 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
15:08:18.307 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 @ 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=
15:08:18.308 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 @ 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=
15:08:18.309 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:08:18.309 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
15:08:18.309 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:08:18.309 WARN  Funcotator - ================================================================================
15:08:18.309 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:08:18.309 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:08:18.309 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:08:18.309 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:08:18.309 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:08:18.309 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:08:18.309 WARN  Funcotator - --------------------------------------------------------------------------------
15:08:18.309 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:08:18.309 WARN  Funcotator -  run was misconfigured.     
15:08:18.309 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:08:18.309 WARN  Funcotator - ================================================================================
15:08:18.309 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:08:18.310 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:18 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2761949184
15:08:18.408 INFO  Funcotator - ------------------------------------------------------------
15:08:18.408 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:18.408 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:18.408 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:18.408 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:18.408 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:18 PM GMT
15:08:18.408 INFO  Funcotator - ------------------------------------------------------------
15:08:18.408 INFO  Funcotator - ------------------------------------------------------------
15:08:18.408 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:18.408 INFO  Funcotator - Picard Version: 3.4.0
15:08:18.408 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:18.408 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:18.408 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:18.408 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:18.408 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:18.408 INFO  Funcotator - Deflater: IntelDeflater
15:08:18.408 INFO  Funcotator - Inflater: IntelInflater
15:08:18.408 INFO  Funcotator - GCS max retries/reopens: 20
15:08:18.408 INFO  Funcotator - Requester pays: disabled
15:08:18.409 INFO  Funcotator - Initializing engine
15:08:18.410 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/M2_test_custom_maf_fields.vcf
15:08:18.411 INFO  Funcotator - Done initializing engine
15:08:18.411 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:18.411 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:18.411 INFO  Funcotator - Initializing data sources...
15:08:18.411 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:18.411 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:18.411 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
15:08:18.411 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
15:08:18.411 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:08:18.411 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:18.411 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
15:08:18.411 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:18.412 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
15:08:18.412 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
15:08:18.413 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:08:18.413 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:18.413 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:08:18.414 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:08:18.415 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:08:18.416 INFO  Funcotator - Initializing Funcotator Engine...
15:08:18.416 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:18.416 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.
15:08:18.416 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out14998729421810268240.maf
15:08:18.417 INFO  ProgressMeter - Starting traversal
15:08:18.417 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:18.418 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909683 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
15:08:18.419 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:10909693-10909698 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
15:08:18.419 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:11058129 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
15:08:18.421 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44515611 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=
15:08:18.422 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:44524478 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=
15:08:18.424 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 3:46640880 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=
15:08:18.424 INFO  ProgressMeter -             unmapped              0.0                     6          51428.6
15:08:18.424 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:08:18.424 WARN  Funcotator - ================================================================================
15:08:18.424 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:08:18.424 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:08:18.424 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:08:18.424 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:08:18.424 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:08:18.424 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:08:18.424 WARN  Funcotator - --------------------------------------------------------------------------------
15:08:18.424 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:08:18.424 WARN  Funcotator -  run was misconfigured.     
15:08:18.424 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:08:18.424 WARN  Funcotator - ================================================================================
15:08:18.424 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:08:18.425 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:18 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2761949184
15:08:18.560 INFO  Funcotator - ------------------------------------------------------------
15:08:18.560 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:18.560 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:18.560 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:18.560 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:18.560 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:18 PM GMT
15:08:18.560 INFO  Funcotator - ------------------------------------------------------------
15:08:18.560 INFO  Funcotator - ------------------------------------------------------------
15:08:18.561 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:18.561 INFO  Funcotator - Picard Version: 3.4.0
15:08:18.561 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:18.561 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:18.561 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:18.561 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:18.561 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:18.561 INFO  Funcotator - Deflater: IntelDeflater
15:08:18.561 INFO  Funcotator - Inflater: IntelInflater
15:08:18.561 INFO  Funcotator - GCS max retries/reopens: 20
15:08:18.561 INFO  Funcotator - Requester pays: disabled
15:08:18.561 INFO  Funcotator - Initializing engine
15:08:18.562 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
15:08:18.563 INFO  Funcotator - Done initializing engine
15:08:18.563 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:18.563 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:18.563 INFO  Funcotator - Initializing data sources...
15:08:18.563 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:18.563 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:18.563 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
15:08:18.563 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
15:08:18.563 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
15:08:18.563 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:18.563 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
15:08:18.563 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:18.564 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
15:08:18.564 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
15:08:18.565 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
15:08:18.565 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:18.565 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
15:08:18.566 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
15:08:18.567 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
15:08:18.568 INFO  Funcotator - Initializing Funcotator Engine...
15:08:18.568 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:18.568 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.
15:08:18.568 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out623597301345918752.maf
15:08:18.568 INFO  ProgressMeter - Starting traversal
15:08:18.568 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:18.570 WARN  MafOutputRenderer - 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
15:08:18.571 WARN  MafOutputRenderer - 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
15:08:18.571 WARN  MafOutputRenderer - 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
15:08:18.572 WARN  MafOutputRenderer - 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=
15:08:18.573 WARN  MafOutputRenderer - 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=
15:08:18.574 WARN  MafOutputRenderer - 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=
15:08:18.574 INFO  ProgressMeter -             unmapped              0.0                     6          60000.0
15:08:18.574 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:08:18.574 WARN  Funcotator - ================================================================================
15:08:18.574 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:08:18.574 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:08:18.574 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:08:18.574 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:08:18.574 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:08:18.574 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:08:18.574 WARN  Funcotator - --------------------------------------------------------------------------------
15:08:18.574 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:08:18.574 WARN  Funcotator -  run was misconfigured.     
15:08:18.574 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:08:18.574 WARN  Funcotator - ================================================================================
15:08:18.574 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:08:18.574 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:18 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2761949184
15:08:18.668 INFO  Funcotator - ------------------------------------------------------------
15:08:18.668 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:18.668 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:18.668 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:18.668 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:18.668 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:18 PM GMT
15:08:18.668 INFO  Funcotator - ------------------------------------------------------------
15:08:18.668 INFO  Funcotator - ------------------------------------------------------------
15:08:18.668 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:18.668 INFO  Funcotator - Picard Version: 3.4.0
15:08:18.668 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:18.668 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:18.668 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:18.668 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:18.668 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:18.668 INFO  Funcotator - Deflater: IntelDeflater
15:08:18.668 INFO  Funcotator - Inflater: IntelInflater
15:08:18.668 INFO  Funcotator - GCS max retries/reopens: 20
15:08:18.668 INFO  Funcotator - Requester pays: disabled
15:08:18.668 INFO  Funcotator - Initializing engine
15:08:18.669 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
15:08:18.671 INFO  Funcotator - Done initializing engine
15:08:18.671 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:18.671 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:18.671 INFO  Funcotator - Initializing data sources...
15:08:18.671 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:18.671 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:18.671 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
15:08:18.671 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
15:08:18.672 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
15:08:18.672 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:18.672 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
15:08:18.672 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:18.673 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
15:08:18.673 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
15:08:18.673 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
15:08:18.673 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:18.674 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
15:08:18.675 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
15:08:18.677 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
15:08:18.678 INFO  Funcotator - Initializing Funcotator Engine...
15:08:18.678 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:18.678 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.
15:08:18.678 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out1809914066057302192.maf
15:08:18.679 INFO  ProgressMeter - Starting traversal
15:08:18.679 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:18.681 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
15:08:18.682 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
15:08:18.682 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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
15:08:18.684 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 @ 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=
15:08:18.685 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:08:18.687 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:08:18.687 INFO  ProgressMeter -             unmapped              0.0                     6          45000.0
15:08:18.687 INFO  ProgressMeter - Traversal complete. Processed 6 total variants in 0.0 minutes.
15:08:18.687 WARN  Funcotator - ================================================================================
15:08:18.687 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:08:18.687 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:08:18.687 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:08:18.687 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:08:18.687 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:08:18.687 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:08:18.687 WARN  Funcotator - --------------------------------------------------------------------------------
15:08:18.687 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:08:18.687 WARN  Funcotator -  run was misconfigured.     
15:08:18.687 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:08:18.687 WARN  Funcotator - ================================================================================
15:08:18.687 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:08:18.687 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:18 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2761949184
15:08:18.784 INFO  Funcotator - ------------------------------------------------------------
15:08:18.784 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:18.784 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:18.784 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:18.784 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:18.784 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:18 PM GMT
15:08:18.784 INFO  Funcotator - ------------------------------------------------------------
15:08:18.784 INFO  Funcotator - ------------------------------------------------------------
15:08:18.784 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:18.784 INFO  Funcotator - Picard Version: 3.4.0
15:08:18.784 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:18.784 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:18.784 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:18.784 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:18.784 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:18.784 INFO  Funcotator - Deflater: IntelDeflater
15:08:18.784 INFO  Funcotator - Inflater: IntelInflater
15:08:18.784 INFO  Funcotator - GCS max retries/reopens: 20
15:08:18.784 INFO  Funcotator - Requester pays: disabled
15:08:18.784 INFO  Funcotator - Initializing engine
15:08:18.785 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:08:18.786 INFO  Funcotator - Done initializing engine
15:08:18.786 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:18.786 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:18.786 INFO  Funcotator - Initializing data sources...
15:08:18.786 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:18.786 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:18.787 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
15:08:18.787 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
15:08:18.787 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
15:08:18.787 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:18.787 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
15:08:18.787 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:18.788 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
15:08:18.788 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
15:08:18.788 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
15:08:18.788 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:18.789 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
15:08:18.789 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
15:08:18.791 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
15:08:18.791 INFO  Funcotator - Initializing Funcotator Engine...
15:08:18.792 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:18.792 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.
15:08:18.792 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6776257078853517446.vcf
15:08:18.795 INFO  ProgressMeter - Starting traversal
15:08:18.795 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:18.805 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
15:08:18.805 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:08:18.805 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:08:18.808 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:18 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2761949184
15:08:18.808 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out6776257078853517446.vcf
15:08:18.898 INFO  Funcotator - ------------------------------------------------------------
15:08:18.898 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:18.898 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:18.898 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:18.898 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:18.899 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:18 PM GMT
15:08:18.899 INFO  Funcotator - ------------------------------------------------------------
15:08:18.899 INFO  Funcotator - ------------------------------------------------------------
15:08:18.899 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:18.899 INFO  Funcotator - Picard Version: 3.4.0
15:08:18.899 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:18.899 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:18.899 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:18.899 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:18.899 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:18.899 INFO  Funcotator - Deflater: IntelDeflater
15:08:18.899 INFO  Funcotator - Inflater: IntelInflater
15:08:18.899 INFO  Funcotator - GCS max retries/reopens: 20
15:08:18.899 INFO  Funcotator - Requester pays: disabled
15:08:18.899 INFO  Funcotator - Initializing engine
15:08:18.900 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/Three_sample_somatic.vcf
15:08:18.901 INFO  Funcotator - Done initializing engine
15:08:18.901 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:18.901 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:18.901 INFO  Funcotator - Initializing data sources...
15:08:18.901 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:18.901 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:18.901 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
15:08:18.901 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.PIK3CA_transcript.fasta -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/gencode_pik3ca/hg19/gencode.v19.PIK3CA_transcript.fasta
15:08:18.901 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
15:08:18.901 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:18.901 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
15:08:18.901 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:18.902 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
15:08:18.902 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
15:08:18.903 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:08:18.903 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:18.903 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
15:08:18.904 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
15:08:18.905 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:08:18.906 INFO  Funcotator - Initializing Funcotator Engine...
15:08:18.906 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:18.906 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
15:08:18.906 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out7914856866445306254.maf
15:08:18.907 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:08:18.907 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:18 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2761949184
15:08:18.997 INFO  Funcotator - ------------------------------------------------------------
15:08:18.997 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:18.997 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:18.997 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:18.997 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:18.997 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:18 PM GMT
15:08:18.997 INFO  Funcotator - ------------------------------------------------------------
15:08:18.997 INFO  Funcotator - ------------------------------------------------------------
15:08:18.997 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:18.997 INFO  Funcotator - Picard Version: 3.4.0
15:08:18.997 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:18.997 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:18.997 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:18.997 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:18.997 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:18.997 INFO  Funcotator - Deflater: IntelDeflater
15:08:18.997 INFO  Funcotator - Inflater: IntelInflater
15:08:18.997 INFO  Funcotator - GCS max retries/reopens: 20
15:08:18.997 INFO  Funcotator - Requester pays: disabled
15:08:18.997 INFO  Funcotator - Initializing engine
15:08:18.998 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/spanning_del.vcf
15:08:19.010 INFO  Funcotator - Done initializing engine
15:08:19.010 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:19.010 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:19.010 INFO  Funcotator - Initializing data sources...
15:08:19.010 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:19.010 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:19.011 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
15:08:19.011 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
15:08:19.011 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
15:08:19.011 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:19.011 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
15:08:19.011 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:19.012 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
15:08:19.012 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
15:08:19.012 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
15:08:19.012 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:19.013 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
15:08:19.025 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
15:08:19.033 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
15:08:19.041 INFO  Funcotator - Initializing Funcotator Engine...
15:08:19.047 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:19.047 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out10924986879943216133.maf
15:08:19.047 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
15:08:19.048 INFO  ProgressMeter - Starting traversal
15:08:19.048 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:19.051 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)
15:08:19.052 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)
15:08:19.052 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:19.052 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:08:19.052 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:08:19.052 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199000-179199000 due to alternate allele: *
15:08:19.053 WARN  MafOutputRenderer - 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+
15:08:19.057 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:19.057 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:08:19.057 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:08:19.057 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199001-179199001 due to alternate allele: *
15:08:19.057 WARN  MafOutputRenderer - 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+
15:08:19.057 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)
15:08:19.058 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)
15:08:19.058 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:19.058 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:08:19.058 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:08:19.058 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199002-179199002 due to alternate allele: *
15:08:19.058 WARN  MafOutputRenderer - 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+
15:08:19.058 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)
15:08:19.059 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)
15:08:19.059 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: G)
15:08:19.059 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: A)
15:08:19.059 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:08:19.059 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199003-179199003 due to alternate allele: *
15:08:19.059 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 @ chr3:179199003 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+
15:08:19.060 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:19.060 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:08:19.060 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:08:19.060 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199004-179199004 due to alternate allele: *
15:08:19.060 WARN  MafOutputRenderer - 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+
15:08:19.061 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:19.061 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:08:19.061 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:08:19.061 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199005-179199005 due to alternate allele: *
15:08:19.061 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 @ chr3:179199005 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=
15:08:19.061 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)
15:08:19.062 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)
15:08:19.062 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:08:19.062 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:08:19.062 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:08:19.062 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199006-179199006 due to alternate allele: *
15:08:19.062 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 @ chr3:179199006 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=
15:08:19.062 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)
15:08:19.063 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)
15:08:19.063 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:19.063 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:08:19.063 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:08:19.063 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199007-179199007 due to alternate allele: *
15:08:19.063 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 @ chr3:179199007 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+
15:08:19.064 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: T)
15:08:19.064 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: C)
15:08:19.064 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:08:19.064 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199008-179199008 due to alternate allele: *
15:08:19.064 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 @ chr3:179199008 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+
15:08:19.065 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)
15:08:19.065 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)
15:08:19.065 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, ref allele: A)
15:08:19.065 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 2 (size=4130, alt allele: G)
15:08:19.065 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:08:19.065 WARN  GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr3:179199009-179199009 due to alternate allele: *
15:08:19.065 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 @ chr3:179199009 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=
15:08:19.066 INFO  ProgressMeter -             unmapped              0.0                    10          33333.3
15:08:19.066 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
15:08:19.066 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/0
15:08:19.066 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:19 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2761949184
[May 27, 2025 at 3:08:19 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2761949184
15:08:19.286 INFO  Funcotator - ------------------------------------------------------------
15:08:19.286 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:19.286 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:19.286 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:19.286 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:19.286 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:19 PM GMT
15:08:19.286 INFO  Funcotator - ------------------------------------------------------------
15:08:19.286 INFO  Funcotator - ------------------------------------------------------------
15:08:19.287 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:19.287 INFO  Funcotator - Picard Version: 3.4.0
15:08:19.287 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:19.287 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:19.287 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:19.287 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:19.287 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:19.287 INFO  Funcotator - Deflater: IntelDeflater
15:08:19.287 INFO  Funcotator - Inflater: IntelInflater
15:08:19.287 INFO  Funcotator - GCS max retries/reopens: 20
15:08:19.287 INFO  Funcotator - Requester pays: disabled
15:08:19.287 INFO  Funcotator - Initializing engine
15:08:19.288 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
15:08:19.290 INFO  Funcotator - Done initializing engine
15:08:19.290 INFO  Funcotator - Validating sequence dictionaries...
15:08:19.290 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:19 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2761949184
15:08:19.387 INFO  Funcotator - ------------------------------------------------------------
15:08:19.387 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:19.387 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:19.387 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:19.387 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:19.387 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:19 PM GMT
15:08:19.387 INFO  Funcotator - ------------------------------------------------------------
15:08:19.387 INFO  Funcotator - ------------------------------------------------------------
15:08:19.387 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:19.387 INFO  Funcotator - Picard Version: 3.4.0
15:08:19.387 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:19.387 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:19.387 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:19.387 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:19.387 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:19.387 INFO  Funcotator - Deflater: IntelDeflater
15:08:19.387 INFO  Funcotator - Inflater: IntelInflater
15:08:19.387 INFO  Funcotator - GCS max retries/reopens: 20
15:08:19.387 INFO  Funcotator - Requester pays: disabled
15:08:19.387 INFO  Funcotator - Initializing engine
15:08:19.389 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
15:08:19.390 INFO  Funcotator - Done initializing engine
15:08:19.390 INFO  Funcotator - Validating sequence dictionaries...
15:08:19.391 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:19.391 INFO  Funcotator - Initializing data sources...
15:08:19.391 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:19.391 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:19.391 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:19.391 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:19.391 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:19.391 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:19.392 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:19.392 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:19.392 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:19.392 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:19.392 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:19.392 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:19.392 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:19.393 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:19.393 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:19.393 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:19.393 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:19.393 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:19.393 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
15:08:19.393 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
15:08:19.414 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:19.415 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
15:08:19.462 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:19.463 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:20.099 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:20.099 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:20.100 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:20.102 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:20.105 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:20.107 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:20.107 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:20.108 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:20.135 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:20.135 INFO  DataSourceUtils - 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 15:08:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:20.135 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:20.174 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:20.175 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:20.175 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:20.217 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:20.217 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:20.217 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:20.218 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:20.218 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:20.324 INFO  Funcotator - Initializing Funcotator Engine...
15:08:20.324 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:08:20.324 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.
15:08:20.324 INFO  Funcotator - Creating a VCF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator1697941878604185074.vcf
15:08:20.326 INFO  ProgressMeter - Starting traversal
15:08:20.326 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:22.257 INFO  ProgressMeter -             unmapped              0.0                   198           6152.3
15:08:22.257 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:08:22.258 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:08:22.266 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:22 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2973761536
15:08:22.353 INFO  Funcotator - ------------------------------------------------------------
15:08:22.353 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:22.353 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:22.353 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:22.353 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:22.353 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:22 PM GMT
15:08:22.353 INFO  Funcotator - ------------------------------------------------------------
15:08:22.353 INFO  Funcotator - ------------------------------------------------------------
15:08:22.353 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:22.353 INFO  Funcotator - Picard Version: 3.4.0
15:08:22.353 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:22.353 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:22.353 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:22.353 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:22.353 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:22.353 INFO  Funcotator - Deflater: IntelDeflater
15:08:22.353 INFO  Funcotator - Inflater: IntelInflater
15:08:22.353 INFO  Funcotator - GCS max retries/reopens: 20
15:08:22.353 INFO  Funcotator - Requester pays: disabled
15:08:22.353 INFO  Funcotator - Initializing engine
15:08:22.355 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/regressionTestVariantSet1.vcf
15:08:22.356 INFO  Funcotator - Done initializing engine
15:08:22.356 INFO  Funcotator - Validating sequence dictionaries...
15:08:22.356 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:22.356 INFO  Funcotator - Initializing data sources...
15:08:22.356 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:22.356 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:22.357 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:22.357 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:22.357 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:22.357 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
15:08:22.357 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:22.357 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:22.358 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:22.358 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:22.358 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:22.358 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:22.358 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:22.358 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:22.359 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:22.359 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:22.359 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:22.359 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:22.359 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:22.359 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:22.379 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:22.379 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:22.425 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:22.426 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:23.023 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:23.023 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:23.024 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:23.026 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:23.028 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:23.030 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:23.031 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
15:08:23.031 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:23.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:23.059 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:08:23	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:23.060 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:23.097 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:23.097 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:23.098 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:23.105 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:23.106 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:23.106 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:23.107 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:23.107 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:23.195 INFO  Funcotator - Initializing Funcotator Engine...
15:08:23.195 INFO  FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode.  Performing conversion. (NOTE: the output VCF will still be B37)
15:08:23.195 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.
15:08:23.195 INFO  Funcotator - Creating a MAF file for output: file:/tmp/regressionTestVariantSet1.vcf.funcotator11494283904666278219.maf
15:08:23.196 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
15:08:23.196 INFO  ProgressMeter - Starting traversal
15:08:23.196 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:25.072 INFO  ProgressMeter -             unmapped              0.0                   198           6332.6
15:08:25.072 INFO  ProgressMeter - Traversal complete. Processed 198 total variants in 0.0 minutes.
15:08:25.072 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/164
15:08:25.072 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:25 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2973761536
15:08:25.165 INFO  Funcotator - ------------------------------------------------------------
15:08:25.166 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:25.166 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:25.166 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:25.166 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:25.166 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:25 PM GMT
15:08:25.166 INFO  Funcotator - ------------------------------------------------------------
15:08:25.166 INFO  Funcotator - ------------------------------------------------------------
15:08:25.166 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:25.166 INFO  Funcotator - Picard Version: 3.4.0
15:08:25.166 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:25.166 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:25.166 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:25.166 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:25.166 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:25.166 INFO  Funcotator - Deflater: IntelDeflater
15:08:25.166 INFO  Funcotator - Inflater: IntelInflater
15:08:25.166 INFO  Funcotator - GCS max retries/reopens: 20
15:08:25.166 INFO  Funcotator - Requester pays: disabled
15:08:25.166 INFO  Funcotator - Initializing engine
15:08:25.193 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/badDataOneAlleleDepthValue_hg38.vcf
15:08:25.212 INFO  Funcotator - Done initializing engine
15:08:25.212 INFO  Funcotator - Validating sequence dictionaries...
15:08:25.218 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:25.218 INFO  Funcotator - Initializing data sources...
15:08:25.218 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:25.218 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:25.219 INFO  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
15:08:25.219 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
15:08:25.219 INFO  DataSourceUtils - Resolved data source 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
15:08:25.219 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
15:08:25.219 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
15:08:25.219 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
15:08:25.220 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
15:08:25.220 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
15:08:25.220 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
15:08:25.220 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
15:08:25.220 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
15:08:25.220 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
15:08:25.220 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
15:08:25.221 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:25.221 INFO  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
15:08:25.221 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
15:08:25.241 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/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:25.241 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
15:08:25.286 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
15:08:25.287 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
15:08:25.876 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
15:08:25.876 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:25.877 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:08:25.878 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
15:08:25.880 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg38/dbSnp.regressionTestSet.hg38.vcf.gz
15:08:25.881 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
15:08:25.945 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38/dnaRepairGenes.20171221T103938.csv
15:08:25.945 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg38/achilles_lineage_results.import.txt
15:08:25.945 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
15:08:25.952 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
15:08:25.952 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:25.953 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg38/gencode.v28.regressionTestVariantSet.gtf
15:08:25.954 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
15:08:25.954 INFO  Funcotator - Initializing Funcotator Engine...
15:08:25.958 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:25.958 INFO  Funcotator - Creating a MAF file for output: file:/tmp/symbollic_allele_proof_input.vcf.funcotator1938237408816065647.vcf
15:08:25.959 INFO  ProgressMeter - Starting traversal
15:08:25.959 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:25.963 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
15:08:25.966 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:25 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2973761536
15:08:26.053 INFO  Funcotator - ------------------------------------------------------------
15:08:26.053 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:26.053 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:26.053 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:26.053 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:26.053 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:26 PM GMT
15:08:26.053 INFO  Funcotator - ------------------------------------------------------------
15:08:26.053 INFO  Funcotator - ------------------------------------------------------------
15:08:26.053 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:26.054 INFO  Funcotator - Picard Version: 3.4.0
15:08:26.054 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:26.054 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:26.054 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:26.054 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:26.054 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:26.054 INFO  Funcotator - Deflater: IntelDeflater
15:08:26.054 INFO  Funcotator - Inflater: IntelInflater
15:08:26.054 INFO  Funcotator - GCS max retries/reopens: 20
15:08:26.054 INFO  Funcotator - Requester pays: disabled
15:08:26.054 INFO  Funcotator - Initializing engine
15:08:26.056 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/vcfBugRepro.vcf
15:08:26.056 INFO  Funcotator - Done initializing engine
15:08:26.056 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:26.056 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:26.056 INFO  Funcotator - Initializing data sources...
15:08:26.056 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/
15:08:26.056 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:26.057 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
15:08:26.057 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
15:08:26.057 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
15:08:26.057 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:26.057 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
15:08:26.057 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSnp : 100000
15:08:26.058 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
15:08:26.058 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
15:08:26.058 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/dbSnp/hg19/dbSnp.repro.vcf
15:08:26.059 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
15:08:26.059 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:26.060 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/vcfFuncotationOrderingBugRepro/gencode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
15:08:26.060 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
15:08:26.060 INFO  Funcotator - Initializing Funcotator Engine...
15:08:26.060 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:26.060 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
15:08:26.060 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:26.060 INFO  Funcotator - Creating a VCF file for output: file:/tmp/tmpTestFilterParsing17154455977713435891.vcf
15:08:26.061 INFO  ProgressMeter - Starting traversal
15:08:26.061 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:26.065 INFO  ProgressMeter -             unmapped              0.0                     1          15000.0
15:08:26.065 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:08:26.065 INFO  VcfFuncotationFactory - dbSnp fake cache hits/total: 0/1
15:08:26.067 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:08:26.068 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/tmpTestFilterParsing17154455977713435891.vcf
15:08:26.155 INFO  Funcotator - ------------------------------------------------------------
15:08:26.155 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:26.155 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:26.155 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:26.155 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:26.155 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:26 PM GMT
15:08:26.155 INFO  Funcotator - ------------------------------------------------------------
15:08:26.155 INFO  Funcotator - ------------------------------------------------------------
15:08:26.156 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:26.156 INFO  Funcotator - Picard Version: 3.4.0
15:08:26.156 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:26.156 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:26.156 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:26.156 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:26.156 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:26.156 INFO  Funcotator - Deflater: IntelDeflater
15:08:26.156 INFO  Funcotator - Inflater: IntelInflater
15:08:26.156 INFO  Funcotator - GCS max retries/reopens: 20
15:08:26.156 INFO  Funcotator - Requester pays: disabled
15:08:26.156 INFO  Funcotator - Initializing engine
15:08:26.157 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:08:26.158 INFO  Funcotator - Done initializing engine
15:08:26.158 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:26.158 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:26.158 INFO  Funcotator - Initializing data sources...
15:08:26.158 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:26.158 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:26.158 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
15:08:26.159 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
15:08:26.159 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
15:08:26.159 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:26.159 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
15:08:26.159 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:26.159 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
15:08:26.160 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
15:08:26.160 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
15:08:26.160 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:26.160 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
15:08:26.161 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
15:08:26.162 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
15:08:26.163 INFO  Funcotator - Initializing Funcotator Engine...
15:08:26.163 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:26.163 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.
15:08:26.163 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out3072948553425891683.maf
15:08:26.164 INFO  ProgressMeter - Starting traversal
15:08:26.164 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:26.166 WARN  MafOutputRenderer - 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=
15:08:26.167 WARN  MafOutputRenderer - 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=
15:08:26.167 WARN  MafOutputRenderer - 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=
15:08:26.167 WARN  MafOutputRenderer - 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=
15:08:26.168 WARN  MafOutputRenderer - 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=
15:08:26.168 WARN  MafOutputRenderer - 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=
15:08:26.169 WARN  MafOutputRenderer - 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=
15:08:26.169 WARN  MafOutputRenderer - 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=
15:08:26.169 WARN  MafOutputRenderer - 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=
15:08:26.170 WARN  MafOutputRenderer - 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=
15:08:26.170 WARN  MafOutputRenderer - 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=
15:08:26.171 WARN  MafOutputRenderer - 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=
15:08:26.171 WARN  MafOutputRenderer - 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=
15:08:26.171 WARN  MafOutputRenderer - 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=
15:08:26.172 WARN  MafOutputRenderer - 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=
15:08:26.172 WARN  MafOutputRenderer - 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=
15:08:26.172 WARN  MafOutputRenderer - 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=
15:08:26.173 WARN  MafOutputRenderer - 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=
15:08:26.173 WARN  MafOutputRenderer - 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=
15:08:26.173 WARN  MafOutputRenderer - 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=
15:08:26.173 WARN  MafOutputRenderer - 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=
15:08:26.174 INFO  ProgressMeter -             unmapped              0.0                    21         126000.0
15:08:26.174 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:08:26.174 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:08:26.174 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:08:26.177 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
15:08:26.178 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:08:26.268 INFO  Funcotator - ------------------------------------------------------------
15:08:26.268 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:26.268 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:26.268 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:26.268 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:26.268 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:26 PM GMT
15:08:26.268 INFO  Funcotator - ------------------------------------------------------------
15:08:26.268 INFO  Funcotator - ------------------------------------------------------------
15:08:26.268 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:26.268 INFO  Funcotator - Picard Version: 3.4.0
15:08:26.268 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:26.268 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:26.268 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:26.268 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:26.268 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:26.268 INFO  Funcotator - Deflater: IntelDeflater
15:08:26.268 INFO  Funcotator - Inflater: IntelInflater
15:08:26.268 INFO  Funcotator - GCS max retries/reopens: 20
15:08:26.268 INFO  Funcotator - Requester pays: disabled
15:08:26.268 INFO  Funcotator - Initializing engine
15:08:26.269 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:08:26.270 INFO  Funcotator - Done initializing engine
15:08:26.270 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:26.270 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:26.270 INFO  Funcotator - Initializing data sources...
15:08:26.270 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:26.270 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:26.270 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
15:08:26.270 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
15:08:26.271 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
15:08:26.271 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:26.271 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
15:08:26.271 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:26.271 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
15:08:26.272 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
15:08:26.272 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
15:08:26.272 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:26.272 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
15:08:26.273 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
15:08:26.274 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
15:08:26.275 INFO  Funcotator - Initializing Funcotator Engine...
15:08:26.275 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:26.275 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.
15:08:26.275 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out1554459551717283180.vcf
15:08:26.279 INFO  ProgressMeter - Starting traversal
15:08:26.279 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:26.287 INFO  ProgressMeter -             unmapped              0.0                    21         157500.0
15:08:26.287 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:08:26.287 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:08:26.290 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:08:26.290 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out1554459551717283180.vcf
15:08:26.415 INFO  Funcotator - ------------------------------------------------------------
15:08:26.415 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:26.415 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:26.415 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:26.415 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:26.415 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:26 PM GMT
15:08:26.415 INFO  Funcotator - ------------------------------------------------------------
15:08:26.415 INFO  Funcotator - ------------------------------------------------------------
15:08:26.415 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:26.415 INFO  Funcotator - Picard Version: 3.4.0
15:08:26.415 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:26.415 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:26.415 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:26.415 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:26.415 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:26.415 INFO  Funcotator - Deflater: IntelDeflater
15:08:26.415 INFO  Funcotator - Inflater: IntelInflater
15:08:26.415 INFO  Funcotator - GCS max retries/reopens: 20
15:08:26.415 INFO  Funcotator - Requester pays: disabled
15:08:26.415 INFO  Funcotator - Initializing engine
15:08:26.416 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
15:08:26.417 INFO  Funcotator - Done initializing engine
15:08:26.417 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:26.417 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:26.417 INFO  Funcotator - Initializing data sources...
15:08:26.417 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:26.417 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:26.417 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
15:08:26.417 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
15:08:26.417 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
15:08:26.417 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:26.417 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
15:08:26.417 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:26.418 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
15:08:26.418 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
15:08:26.419 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
15:08:26.419 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:26.419 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
15:08:26.420 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
15:08:26.421 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
15:08:26.422 INFO  Funcotator - Initializing Funcotator Engine...
15:08:26.422 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:26.422 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.
15:08:26.422 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:26.422 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out6468293984817411900.vcf
15:08:26.422 INFO  ProgressMeter - Starting traversal
15:08:26.422 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:26.427 INFO  ProgressMeter -             unmapped              0.0                     5          60000.0
15:08:26.427 INFO  ProgressMeter - Traversal complete. Processed 5 total variants in 0.0 minutes.
15:08:26.427 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:08:26.429 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:08:26.430 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out6468293984817411900.vcf
15:08:26.517 INFO  Funcotator - ------------------------------------------------------------
15:08:26.517 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:26.517 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:26.517 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:26.517 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:26.517 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:26 PM GMT
15:08:26.517 INFO  Funcotator - ------------------------------------------------------------
15:08:26.517 INFO  Funcotator - ------------------------------------------------------------
15:08:26.517 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:26.518 INFO  Funcotator - Picard Version: 3.4.0
15:08:26.518 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:26.518 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:26.518 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:26.518 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:26.518 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:26.518 INFO  Funcotator - Deflater: IntelDeflater
15:08:26.518 INFO  Funcotator - Inflater: IntelInflater
15:08:26.518 INFO  Funcotator - GCS max retries/reopens: 20
15:08:26.518 INFO  Funcotator - Requester pays: disabled
15:08:26.518 INFO  Funcotator - Initializing engine
15:08:26.519 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
15:08:26.519 INFO  Funcotator - Done initializing engine
15:08:26.519 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:26.519 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:26.519 INFO  Funcotator - Initializing data sources...
15:08:26.519 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:26.519 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:26.519 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
15:08:26.519 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
15:08:26.520 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
15:08:26.520 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:26.520 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
15:08:26.520 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:26.520 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
15:08:26.521 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
15:08:26.521 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
15:08:26.521 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:26.522 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
15:08:26.522 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
15:08:26.523 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
15:08:26.524 INFO  Funcotator - Initializing Funcotator Engine...
15:08:26.524 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:26.524 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.
15:08:26.524 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:26.524 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out10629211214289011809.vcf
15:08:26.525 INFO  ProgressMeter - Starting traversal
15:08:26.525 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:26.533 INFO  ProgressMeter -             unmapped              0.0                    15         112500.0
15:08:26.533 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
15:08:26.533 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
15:08:26.535 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:08:26.621 INFO  Funcotator - ------------------------------------------------------------
15:08:26.621 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:26.621 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:26.621 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:26.621 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:26.621 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:26 PM GMT
15:08:26.621 INFO  Funcotator - ------------------------------------------------------------
15:08:26.621 INFO  Funcotator - ------------------------------------------------------------
15:08:26.621 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:26.621 INFO  Funcotator - Picard Version: 3.4.0
15:08:26.621 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:26.621 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:26.621 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:26.621 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:26.621 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:26.621 INFO  Funcotator - Deflater: IntelDeflater
15:08:26.621 INFO  Funcotator - Inflater: IntelInflater
15:08:26.621 INFO  Funcotator - GCS max retries/reopens: 20
15:08:26.621 INFO  Funcotator - Requester pays: disabled
15:08:26.621 INFO  Funcotator - Initializing engine
15:08:26.622 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_SNPS_3.vcf
15:08:26.623 INFO  Funcotator - Done initializing engine
15:08:26.623 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:26.623 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:26.623 INFO  Funcotator - Initializing data sources...
15:08:26.623 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:26.623 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:26.623 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
15:08:26.623 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
15:08:26.623 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
15:08:26.623 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:26.623 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
15:08:26.623 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:26.624 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
15:08:26.624 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
15:08:26.625 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
15:08:26.625 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:26.626 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
15:08:26.627 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
15:08:26.628 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
15:08:26.629 INFO  Funcotator - Initializing Funcotator Engine...
15:08:26.629 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:26.629 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.
15:08:26.629 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:26.629 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out5213439380703980518.maf
15:08:26.629 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
15:08:26.630 INFO  ProgressMeter - Starting traversal
15:08:26.630 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:26.632 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
15:08:26.633 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:08:26.634 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916617 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:08:26.634 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178919220 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:08:26.635 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178921433 Q40.00 of type=SNP alleles=[A*, T] attr={} GT=[] filters=
15:08:26.635 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178922366 Q40.00 of type=SNP alleles=[T*, A] attr={} GT=[] filters=
15:08:26.635 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178928317 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:08:26.636 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178936091 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
15:08:26.636 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178937063 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:08:26.636 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178941890 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
15:08:26.637 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178942511 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:08:26.637 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178942523 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
15:08:26.637 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178943785 Q40.00 of type=SNP alleles=[C*, T] attr={} GT=[] filters=
15:08:26.638 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178947158 Q40.00 of type=SNP alleles=[G*, A] attr={} GT=[] filters=
15:08:26.638 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178952085 Q40.00 of type=SNP alleles=[A*, T] attr={} GT=[] filters=
15:08:26.638 INFO  ProgressMeter -             unmapped              0.0                    15         112500.0
15:08:26.638 INFO  ProgressMeter - Traversal complete. Processed 15 total variants in 0.0 minutes.
15:08:26.638 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/3
15:08:26.638 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:08:26.639 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out10629211214289011809.vcf
15:08:26.729 INFO  Funcotator - ------------------------------------------------------------
15:08:26.729 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:26.729 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:26.729 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:26.729 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:26.729 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:26 PM GMT
15:08:26.729 INFO  Funcotator - ------------------------------------------------------------
15:08:26.729 INFO  Funcotator - ------------------------------------------------------------
15:08:26.729 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:26.729 INFO  Funcotator - Picard Version: 3.4.0
15:08:26.729 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:26.729 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:26.729 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:26.729 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:26.729 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:26.729 INFO  Funcotator - Deflater: IntelDeflater
15:08:26.729 INFO  Funcotator - Inflater: IntelInflater
15:08:26.729 INFO  Funcotator - GCS max retries/reopens: 20
15:08:26.729 INFO  Funcotator - Requester pays: disabled
15:08:26.729 INFO  Funcotator - Initializing engine
15:08:26.730 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
15:08:26.731 INFO  Funcotator - Done initializing engine
15:08:26.731 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:26.731 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:26.731 INFO  Funcotator - Initializing data sources...
15:08:26.731 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:26.731 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:26.731 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
15:08:26.731 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
15:08:26.731 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
15:08:26.731 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:26.731 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
15:08:26.732 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:26.732 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
15:08:26.732 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
15:08:26.733 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
15:08:26.733 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:26.733 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
15:08:26.734 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
15:08:26.735 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
15:08:26.736 INFO  Funcotator - Initializing Funcotator Engine...
15:08:26.736 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:26.736 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.
15:08:26.736 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:26.736 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out17031144895062925982.vcf
15:08:26.737 INFO  ProgressMeter - Starting traversal
15:08:26.737 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:26.767 INFO  ProgressMeter -             unmapped              0.0                    57         114000.0
15:08:26.767 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:08:26.767 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:08:26.770 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:08:26.857 INFO  Funcotator - ------------------------------------------------------------
15:08:26.857 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:26.857 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:26.857 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:26.857 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:26.857 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:26 PM GMT
15:08:26.857 INFO  Funcotator - ------------------------------------------------------------
15:08:26.857 INFO  Funcotator - ------------------------------------------------------------
15:08:26.857 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:26.857 INFO  Funcotator - Picard Version: 3.4.0
15:08:26.857 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:26.857 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:26.857 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:26.857 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:26.857 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:26.857 INFO  Funcotator - Deflater: IntelDeflater
15:08:26.857 INFO  Funcotator - Inflater: IntelInflater
15:08:26.857 INFO  Funcotator - GCS max retries/reopens: 20
15:08:26.857 INFO  Funcotator - Requester pays: disabled
15:08:26.857 INFO  Funcotator - Initializing engine
15:08:26.858 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
15:08:26.859 INFO  Funcotator - Done initializing engine
15:08:26.859 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:26.859 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:26.859 INFO  Funcotator - Initializing data sources...
15:08:26.859 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:08:26.859 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:26.859 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
15:08:26.859 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
15:08:26.859 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
15:08:26.859 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:26.859 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
15:08:26.859 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:26.860 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
15:08:26.860 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
15:08:26.861 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:08:26.861 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:08:26.861 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
15:08:26.862 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dummy_clinvar_hg19_pik3ca.vcf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:08:26.863 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/dummy_clinvar_pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
15:08:26.864 INFO  Funcotator - Initializing Funcotator Engine...
15:08:26.864 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:08:26.864 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
15:08:26.864 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:26.864 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out14990332412831529391.maf
15:08:26.865 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
15:08:26.865 INFO  ProgressMeter - Starting traversal
15:08:26.865 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:26.869 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCGA] attr={} GT=[] filters=
15:08:26.870 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGAG] attr={} GT=[] filters=
15:08:26.870 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948165 Q40.00 of type=INDEL alleles=[G*, GT] attr={} GT=[] filters=
15:08:26.870 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948166 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
15:08:26.871 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TCG] attr={} GT=[] filters=
15:08:26.872 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948159 Q40.00 of type=INDEL alleles=[T*, TGA] attr={} GT=[] filters=
15:08:26.872 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
15:08:26.873 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948154 Q40.00 of type=INDEL alleles=[G*, GGAATT] attr={} GT=[] filters=
15:08:26.873 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948155 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
15:08:26.874 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948156 Q40.00 of type=INDEL alleles=[A*, AGAATT] attr={} GT=[] filters=
15:08:26.874 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948157 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
15:08:26.874 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948158 Q40.00 of type=INDEL alleles=[T*, TGAATT] attr={} GT=[] filters=
15:08:26.875 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178948163 Q40.00 of type=INDEL alleles=[A*, ATGA] attr={} GT=[] filters=
15:08:26.876 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916937-178916940 Q40.00 of type=INDEL alleles=[TGAA*, T] attr={} GT=[] filters=
15:08:26.877 WARN  MafOutputRenderer - 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=
15:08:26.877 WARN  MafOutputRenderer - 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=
15:08:26.878 WARN  MafOutputRenderer - 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=
15:08:26.878 WARN  MafOutputRenderer - 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=
15:08:26.878 WARN  MafOutputRenderer - 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=
15:08:26.879 WARN  MafOutputRenderer - 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=
15:08:26.880 WARN  MafOutputRenderer - 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=
15:08:26.880 WARN  MafOutputRenderer - 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=
15:08:26.882 WARN  MafOutputRenderer - 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=
15:08:26.882 WARN  MafOutputRenderer - 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=
15:08:26.882 WARN  MafOutputRenderer - 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=
15:08:26.884 WARN  MafOutputRenderer - 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=
15:08:26.884 WARN  MafOutputRenderer - 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=
15:08:26.885 WARN  MafOutputRenderer - 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=
15:08:26.886 WARN  MafOutputRenderer - 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=
15:08:26.886 WARN  MafOutputRenderer - 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=
15:08:26.886 WARN  MafOutputRenderer - 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=
15:08:26.887 WARN  MafOutputRenderer - 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=
15:08:26.888 WARN  MafOutputRenderer - 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=
15:08:26.888 WARN  MafOutputRenderer - 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=
15:08:26.889 WARN  MafOutputRenderer - 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=
15:08:26.890 WARN  MafOutputRenderer - 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=
15:08:26.890 WARN  MafOutputRenderer - 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=
15:08:26.891 WARN  MafOutputRenderer - 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=
15:08:26.892 WARN  MafOutputRenderer - 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=
15:08:26.892 WARN  MafOutputRenderer - 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=
15:08:26.892 WARN  MafOutputRenderer - 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=
15:08:26.894 WARN  MafOutputRenderer - 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=
15:08:26.894 WARN  MafOutputRenderer - 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=
15:08:26.894 WARN  MafOutputRenderer - 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=
15:08:26.895 WARN  MafOutputRenderer - 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=
15:08:26.896 WARN  MafOutputRenderer - 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=
15:08:26.896 WARN  MafOutputRenderer - 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=
15:08:26.897 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 @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
15:08:26.897 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 @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
15:08:26.898 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 @ chr3:178916618-178916622 Q40.00 of type=INDEL alleles=[CTCCA*, C] attr={} GT=[] filters=
15:08:26.899 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 @ chr3:178916619-178916623 Q40.00 of type=INDEL alleles=[TCCAC*, T] attr={} GT=[] filters=
15:08:26.899 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 @ chr3:178916620-178916624 Q40.00 of type=INDEL alleles=[CCACG*, C] attr={} GT=[] filters=
15:08:26.899 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 @ chr3:178916621-178916625 Q40.00 of type=INDEL alleles=[CACGA*, C] attr={} GT=[] filters=
15:08:26.901 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 @ chr3:178916618-178916625 Q40.00 of type=INDEL alleles=[CTCCACGA*, C] attr={} GT=[] filters=
15:08:26.901 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 @ chr3:178916619-178916626 Q40.00 of type=INDEL alleles=[TCCACGAC*, T] attr={} GT=[] filters=
15:08:26.901 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 @ chr3:178916620-178916627 Q40.00 of type=INDEL alleles=[CCACGACC*, C] attr={} GT=[] filters=
15:08:26.902 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 @ chr3:178916621-178916628 Q40.00 of type=INDEL alleles=[CACGACCA*, C] attr={} GT=[] filters=
15:08:26.902 INFO  ProgressMeter -             unmapped              0.0                    57          92432.4
15:08:26.902 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:08:26.902 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:08:26.902 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:26 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:08:26.903 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out17031144895062925982.vcf
15:08:26.999 INFO  Funcotator - ------------------------------------------------------------
15:08:26.999 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:26.999 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:26.999 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:26.999 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:26.999 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:26 PM GMT
15:08:26.999 INFO  Funcotator - ------------------------------------------------------------
15:08:26.999 INFO  Funcotator - ------------------------------------------------------------
15:08:26.999 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:26.999 INFO  Funcotator - Picard Version: 3.4.0
15:08:26.999 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:26.999 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:26.999 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:26.999 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:26.999 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:26.999 INFO  Funcotator - Deflater: IntelDeflater
15:08:26.999 INFO  Funcotator - Inflater: IntelInflater
15:08:26.999 INFO  Funcotator - GCS max retries/reopens: 20
15:08:26.999 INFO  Funcotator - Requester pays: disabled
15:08:26.999 INFO  Funcotator - Initializing engine
15:08:27.000 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
15:08:27.001 INFO  Funcotator - Done initializing engine
15:08:27.001 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:27.001 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:27.001 INFO  Funcotator - Initializing data sources...
15:08:27.001 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:27.001 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:27.001 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
15:08:27.002 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:27.002 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
15:08:27.002 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
15:08:27.002 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
15:08:27.002 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
15:08:27.002 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
15:08:27.003 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
15:08:27.003 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
15:08:27.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:27.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:27.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:27.003 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:27.004 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:27.004 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:27.004 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:27.004 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:27.004 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:27.024 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:27.025 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:27.071 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:27.072 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:27.652 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:27.652 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:27.653 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:27.655 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:27.658 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:27.660 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:27.660 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:27.660 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:27.687 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:27.687 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
WARNING	2025-05-27 15:08:27	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:27.688 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:27.725 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:27.725 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:27.726 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:27.733 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:27.733 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:27.733 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:27.734 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:27.734 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:27.814 INFO  Funcotator - Initializing Funcotator Engine...
15:08:27.814 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:27.814 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:27.814 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out13164273907097273665.vcf
15:08:27.815 INFO  ProgressMeter - Starting traversal
15:08:27.815 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:42.303 INFO  ProgressMeter -        chr19:9077594              0.2                  2000           8282.7
15:08:42.735 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)
15:08:42.736 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)
15:08:43.417 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7910.5
15:08:43.417 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
15:08:43.417 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
15:08:43.418 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:43 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.27 minutes.
Runtime.totalMemory()=2973761536
15:08:43.523 INFO  Funcotator - ------------------------------------------------------------
15:08:43.523 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:08:43.523 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:43.523 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:08:43.523 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:43.523 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:08:43 PM GMT
15:08:43.523 INFO  Funcotator - ------------------------------------------------------------
15:08:43.523 INFO  Funcotator - ------------------------------------------------------------
15:08:43.524 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:08:43.524 INFO  Funcotator - Picard Version: 3.4.0
15:08:43.524 INFO  Funcotator - Built for Spark Version: 3.5.0
15:08:43.524 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:43.524 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:43.524 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:43.524 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:43.524 INFO  Funcotator - Deflater: IntelDeflater
15:08:43.524 INFO  Funcotator - Inflater: IntelInflater
15:08:43.524 INFO  Funcotator - GCS max retries/reopens: 20
15:08:43.524 INFO  Funcotator - Requester pays: disabled
15:08:43.524 INFO  Funcotator - Initializing engine
15:08:43.525 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/MUC16_MNP.vcf
15:08:43.525 INFO  Funcotator - Done initializing engine
15:08:43.525 INFO  Funcotator - Skipping sequence dictionary validation.
15:08:43.525 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:08:43.525 INFO  Funcotator - Initializing data sources...
15:08:43.525 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/
15:08:43.525 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:08:43.526 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:43.526 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:43.526 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:43.526 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:43.527 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:43.527 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:43.527 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:43.527 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:43.527 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:43.528 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:43.528 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:43.528 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:43.528 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:43.528 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:43.528 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:43.528 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:08:43.528 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:08:43.529 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/simple_uniprot_Dec012014.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
15:08:43.556 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:08:43.557 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/hgnc_download_Nov302017.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg19/hgnc_download_Nov302017.tsv
15:08:43.601 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_fusion.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_fusion/hg19/cosmic_fusion.tsv
15:08:43.602 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
15:08:44.184 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:44.184 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
15:08:44.185 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:44.187 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dbSnp.regressionTestSet.hg19.vcf.gz -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:44.190 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dbSnp/hg19/dbSnp.regressionTestSet.hg19.vcf.gz
15:08:44.192 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:08:44.192 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:44.193 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.config
15:08:44.220 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/clinvar_hgmd.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/clinvar/hg19/clinvar_hgmd.tsv
15:08:44.220 INFO  DataSourceUtils - 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 15:08:44	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:08:44.220 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode_xrefseq_v75_37.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
15:08:44.258 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/dnaRepairGenes.20171221T103938.csv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg19/dnaRepairGenes.20171221T103938.csv
15:08:44.258 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/achilles_lineage_results.import.txt -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/achilles/hg19/achilles_lineage_results.import.txt
15:08:44.259 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/cosmic_tissue.tsv -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic_tissue/hg19/cosmic_tissue.tsv
15:08:44.266 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/CosmicTest.db -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/cosmic/hg19/CosmicTest.db
15:08:44.266 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.gtf -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:44.267 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:08:44.267 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.gtf
15:08:44.268 INFO  DataSourceUtils - Resolved data source file path: file:///gatkCloneMountPoint/gencode.v19.testVariantSubset.pc_transcripts.fa -> file:///gatkCloneMountPoint/src/test/resources/large/funcotator/funcotator_dataSources/gencode/hg19/gencode.v19.testVariantSubset.pc_transcripts.fa
15:08:44.347 INFO  Funcotator - Initializing Funcotator Engine...
15:08:44.347 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:08:44.347 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:08:44.347 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out9088222567772013186.maf
15:08:44.347 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
15:08:44.348 INFO  ProgressMeter - Starting traversal
15:08:44.348 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:08:58.730 INFO  ProgressMeter -        chr19:9077594              0.2                  2000           8343.8
15:08:59.155 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)
15:08:59.156 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)
15:08:59.843 INFO  ProgressMeter -        chr19:9077594              0.3                  2057           7965.2
15:08:59.843 INFO  ProgressMeter - Traversal complete. Processed 2057 total variants in 0.3 minutes.
15:08:59.843 INFO  VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/700
15:08:59.844 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:08:59 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.27 minutes.
Runtime.totalMemory()=2973761536
15:08:59.845 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out13164273907097273665.vcf
15:09:00.235 INFO  Funcotator - ------------------------------------------------------------
15:09:00.235 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:09:00.235 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:00.235 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:09:00.235 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:00.235 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:09:00 PM GMT
15:09:00.235 INFO  Funcotator - ------------------------------------------------------------
15:09:00.235 INFO  Funcotator - ------------------------------------------------------------
15:09:00.235 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:09:00.235 INFO  Funcotator - Picard Version: 3.4.0
15:09:00.235 INFO  Funcotator - Built for Spark Version: 3.5.0
15:09:00.235 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:00.235 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:00.235 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:00.235 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:00.235 INFO  Funcotator - Deflater: IntelDeflater
15:09:00.235 INFO  Funcotator - Inflater: IntelInflater
15:09:00.235 INFO  Funcotator - GCS max retries/reopens: 20
15:09:00.235 INFO  Funcotator - Requester pays: disabled
15:09:00.235 INFO  Funcotator - Initializing engine
15:09:00.236 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:09:00.257 INFO  Funcotator - Done initializing engine
15:09:00.257 INFO  Funcotator - Skipping sequence dictionary validation.
15:09:00.257 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:09:00.257 INFO  Funcotator - Initializing data sources...
15:09:00.257 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:09:00.257 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:09:00.257 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
15:09:00.257 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
15:09:00.257 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
15:09:00.257 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:09:00.257 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
15:09:00.257 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:09:00.258 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
15:09:00.258 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
15:09:00.259 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
15:09:00.259 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:09:00.259 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
15:09:00.267 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
15:09:00.275 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
15:09:00.284 INFO  Funcotator - Initializing Funcotator Engine...
15:09:00.290 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:09:00.290 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out17917750827671079190.vcf
15:09:00.302 INFO  ProgressMeter - Starting traversal
15:09:00.302 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:00.325 INFO  ProgressMeter -             unmapped              0.0                   100         260869.6
15:09:00.325 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:09:00.325 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:09:00.330 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:09:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:09:00.418 INFO  Funcotator - ------------------------------------------------------------
15:09:00.418 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:09:00.418 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:00.418 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:09:00.418 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:00.418 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:09:00 PM GMT
15:09:00.418 INFO  Funcotator - ------------------------------------------------------------
15:09:00.418 INFO  Funcotator - ------------------------------------------------------------
15:09:00.418 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:09:00.418 INFO  Funcotator - Picard Version: 3.4.0
15:09:00.418 INFO  Funcotator - Built for Spark Version: 3.5.0
15:09:00.418 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:00.418 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:00.418 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:00.418 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:00.418 INFO  Funcotator - Deflater: IntelDeflater
15:09:00.419 INFO  Funcotator - Inflater: IntelInflater
15:09:00.419 INFO  Funcotator - GCS max retries/reopens: 20
15:09:00.419 INFO  Funcotator - Requester pays: disabled
15:09:00.419 INFO  Funcotator - Initializing engine
15:09:00.419 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/hg38_trio.pik3ca.vcf
15:09:00.435 INFO  Funcotator - Done initializing engine
15:09:00.435 INFO  Funcotator - Skipping sequence dictionary validation.
15:09:00.435 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:09:00.435 INFO  Funcotator - Initializing data sources...
15:09:00.436 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:09:00.436 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:09:00.436 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
15:09:00.436 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
15:09:00.436 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
15:09:00.436 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:09:00.436 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
15:09:00.436 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:09:00.437 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
15:09:00.437 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
15:09:00.437 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
15:09:00.437 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:09:00.438 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
15:09:00.446 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
15:09:00.454 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
15:09:00.462 INFO  Funcotator - Initializing Funcotator Engine...
15:09:00.466 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
15:09:00.466 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out10411971719795931196.maf
15:09:00.467 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
15:09:00.467 INFO  ProgressMeter - Starting traversal
15:09:00.467 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:00.470 WARN  MafOutputRenderer - 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=
15:09:00.474 WARN  MafOutputRenderer - 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=
15:09:00.474 WARN  MafOutputRenderer - 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+
15:09:00.474 WARN  MafOutputRenderer - 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+
15:09:00.475 WARN  MafOutputRenderer - 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+
15:09:00.475 WARN  MafOutputRenderer - 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+
15:09:00.475 WARN  MafOutputRenderer - 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=
15:09:00.476 WARN  MafOutputRenderer - 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=
15:09:00.476 WARN  MafOutputRenderer - 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=
15:09:00.476 WARN  MafOutputRenderer - 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=
15:09:00.476 WARN  MafOutputRenderer - 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=
15:09:00.476 WARN  MafOutputRenderer - 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=
15:09:00.477 WARN  MafOutputRenderer - 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=
15:09:00.477 WARN  MafOutputRenderer - 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=
15:09:00.477 WARN  MafOutputRenderer - 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=
15:09:00.478 WARN  MafOutputRenderer - 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=
15:09:00.478 WARN  MafOutputRenderer - 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=
15:09:00.478 WARN  MafOutputRenderer - 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=
15:09:00.478 WARN  MafOutputRenderer - 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=
15:09:00.479 WARN  MafOutputRenderer - 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+
15:09:00.479 WARN  MafOutputRenderer - 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
15:09:00.479 WARN  MafOutputRenderer - 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=
15:09:00.480 WARN  MafOutputRenderer - 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=
15:09:00.480 WARN  MafOutputRenderer - 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=
15:09:00.480 WARN  MafOutputRenderer - 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=
15:09:00.480 WARN  MafOutputRenderer - 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=
15:09:00.481 WARN  MafOutputRenderer - 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=
15:09:00.481 WARN  MafOutputRenderer - 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=
15:09:00.481 WARN  MafOutputRenderer - 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
15:09:00.481 WARN  MafOutputRenderer - 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=
15:09:00.482 WARN  MafOutputRenderer - 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=
15:09:00.482 WARN  MafOutputRenderer - 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=
15:09:00.482 WARN  MafOutputRenderer - 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=
15:09:00.482 WARN  MafOutputRenderer - 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=
15:09:00.483 WARN  MafOutputRenderer - 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=
15:09:00.483 WARN  MafOutputRenderer - 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=
15:09:00.483 WARN  MafOutputRenderer - 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=
15:09:00.483 WARN  MafOutputRenderer - 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=
15:09:00.484 WARN  MafOutputRenderer - 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=
15:09:00.484 WARN  MafOutputRenderer - 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=
15:09:00.484 WARN  MafOutputRenderer - 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=
15:09:00.485 WARN  MafOutputRenderer - 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=
15:09:00.485 WARN  MafOutputRenderer - 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=
15:09:00.486 WARN  MafOutputRenderer - 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=
15:09:00.486 WARN  MafOutputRenderer - 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=
15:09:00.486 WARN  MafOutputRenderer - 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=
15:09:00.486 WARN  MafOutputRenderer - 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+
15:09:00.487 WARN  MafOutputRenderer - 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=
15:09:00.487 WARN  MafOutputRenderer - 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=
15:09:00.487 WARN  MafOutputRenderer - 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=
15:09:00.487 WARN  MafOutputRenderer - 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=
15:09:00.487 WARN  MafOutputRenderer - 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=
15:09:00.488 WARN  MafOutputRenderer - 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=
15:09:00.488 WARN  MafOutputRenderer - 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=
15:09:00.488 WARN  MafOutputRenderer - 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=
15:09:00.488 WARN  MafOutputRenderer - 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=
15:09:00.488 WARN  MafOutputRenderer - 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=
15:09:00.489 WARN  MafOutputRenderer - 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=
15:09:00.489 WARN  MafOutputRenderer - 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=
15:09:00.489 WARN  MafOutputRenderer - 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=
15:09:00.489 WARN  MafOutputRenderer - 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=
15:09:00.489 WARN  MafOutputRenderer - 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=
15:09:00.490 WARN  MafOutputRenderer - 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=
15:09:00.490 WARN  MafOutputRenderer - 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=
15:09:00.490 WARN  MafOutputRenderer - 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=
15:09:00.490 WARN  MafOutputRenderer - 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=
15:09:00.490 WARN  MafOutputRenderer - 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=
15:09:00.491 WARN  MafOutputRenderer - 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=
15:09:00.491 WARN  MafOutputRenderer - 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=
15:09:00.491 WARN  MafOutputRenderer - 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=
15:09:00.491 WARN  MafOutputRenderer - 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=
15:09:00.491 WARN  MafOutputRenderer - 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=
15:09:00.492 WARN  MafOutputRenderer - 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=
15:09:00.492 WARN  MafOutputRenderer - 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=
15:09:00.492 WARN  MafOutputRenderer - 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=
15:09:00.492 WARN  MafOutputRenderer - 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=
15:09:00.492 WARN  MafOutputRenderer - 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=
15:09:00.492 WARN  MafOutputRenderer - 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=
15:09:00.493 WARN  MafOutputRenderer - 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=
15:09:00.493 WARN  MafOutputRenderer - 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=
15:09:00.493 WARN  MafOutputRenderer - 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=
15:09:00.493 WARN  MafOutputRenderer - 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=
15:09:00.493 WARN  MafOutputRenderer - 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=
15:09:00.494 WARN  MafOutputRenderer - 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=
15:09:00.494 WARN  MafOutputRenderer - 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=
15:09:00.494 WARN  MafOutputRenderer - 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=
15:09:00.494 WARN  MafOutputRenderer - 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=
15:09:00.494 WARN  MafOutputRenderer - 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=
15:09:00.495 WARN  MafOutputRenderer - 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=
15:09:00.495 WARN  MafOutputRenderer - 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=
15:09:00.495 WARN  MafOutputRenderer - 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=
15:09:00.495 WARN  MafOutputRenderer - 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=
15:09:00.495 WARN  MafOutputRenderer - 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=
15:09:00.496 WARN  MafOutputRenderer - 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=
15:09:00.496 WARN  MafOutputRenderer - 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=
15:09:00.496 WARN  MafOutputRenderer - 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=
15:09:00.496 WARN  MafOutputRenderer - 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=
15:09:00.496 WARN  MafOutputRenderer - 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=
15:09:00.497 WARN  MafOutputRenderer - 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=
15:09:00.497 WARN  MafOutputRenderer - 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=
15:09:00.497 INFO  ProgressMeter -             unmapped              0.0                   100         200000.0
15:09:00.497 INFO  ProgressMeter - Traversal complete. Processed 100 total variants in 0.0 minutes.
15:09:00.497 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:09:00.497 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:09:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:09:00.498 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out17917750827671079190.vcf
15:09:00.653 INFO  Funcotator - ------------------------------------------------------------
15:09:00.653 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:09:00.654 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:00.654 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:09:00.654 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:00.654 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:09:00 PM GMT
15:09:00.654 INFO  Funcotator - ------------------------------------------------------------
15:09:00.654 INFO  Funcotator - ------------------------------------------------------------
15:09:00.654 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:09:00.654 INFO  Funcotator - Picard Version: 3.4.0
15:09:00.654 INFO  Funcotator - Built for Spark Version: 3.5.0
15:09:00.654 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:00.654 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:00.654 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:00.654 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:00.654 INFO  Funcotator - Deflater: IntelDeflater
15:09:00.654 INFO  Funcotator - Inflater: IntelInflater
15:09:00.654 INFO  Funcotator - GCS max retries/reopens: 20
15:09:00.654 INFO  Funcotator - Requester pays: disabled
15:09:00.654 INFO  Funcotator - Initializing engine
15:09:00.655 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
15:09:00.655 INFO  Funcotator - Done initializing engine
15:09:00.655 INFO  Funcotator - Skipping sequence dictionary validation.
15:09:00.655 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:09:00.655 INFO  Funcotator - Initializing data sources...
15:09:00.655 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:09:00.655 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:09:00.655 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
15:09:00.655 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
15:09:00.656 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
15:09:00.656 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:09:00.656 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
15:09:00.656 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:09:00.656 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
15:09:00.656 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
15:09:00.657 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
15:09:00.657 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:09:00.657 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
15:09:00.658 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
15:09:00.659 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
15:09:00.660 INFO  Funcotator - Initializing Funcotator Engine...
15:09:00.660 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:09:00.660 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.
15:09:00.660 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:09:00.660 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12781114202615861897.vcf
15:09:00.660 INFO  ProgressMeter - Starting traversal
15:09:00.660 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:00.690 INFO  ProgressMeter -             unmapped              0.0                    57         114000.0
15:09:00.690 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:09:00.690 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:09:00.692 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:09:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:09:00.779 INFO  Funcotator - ------------------------------------------------------------
15:09:00.779 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:09:00.779 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:00.779 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:09:00.779 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:00.780 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:09:00 PM GMT
15:09:00.780 INFO  Funcotator - ------------------------------------------------------------
15:09:00.780 INFO  Funcotator - ------------------------------------------------------------
15:09:00.780 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:09:00.780 INFO  Funcotator - Picard Version: 3.4.0
15:09:00.780 INFO  Funcotator - Built for Spark Version: 3.5.0
15:09:00.780 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:00.780 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:00.780 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:00.780 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:00.780 INFO  Funcotator - Deflater: IntelDeflater
15:09:00.780 INFO  Funcotator - Inflater: IntelInflater
15:09:00.780 INFO  Funcotator - GCS max retries/reopens: 20
15:09:00.780 INFO  Funcotator - Requester pays: disabled
15:09:00.780 INFO  Funcotator - Initializing engine
15:09:00.781 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/PIK3CA_INDELS_3.vcf
15:09:00.781 INFO  Funcotator - Done initializing engine
15:09:00.781 INFO  Funcotator - Skipping sequence dictionary validation.
15:09:00.781 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:09:00.781 INFO  Funcotator - Initializing data sources...
15:09:00.781 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:09:00.781 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:09:00.781 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
15:09:00.781 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
15:09:00.782 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
15:09:00.782 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:09:00.782 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
15:09:00.782 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:09:00.782 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
15:09:00.782 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
15:09:00.783 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
15:09:00.783 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:09:00.783 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
15:09:00.784 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
15:09:00.785 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
15:09:00.786 INFO  Funcotator - Initializing Funcotator Engine...
15:09:00.786 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:09:00.786 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.
15:09:00.786 WARN  FuncotatorUtils - No sequence dictionary provided in the input VCF file.  Cannot check against B37.
15:09:00.786 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out11917202739946825531.maf
15:09:00.786 WARN  MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count).  Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
15:09:00.786 INFO  ProgressMeter - Starting traversal
15:09:00.786 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:00.789 WARN  MafOutputRenderer - 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=
15:09:00.789 WARN  MafOutputRenderer - 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=
15:09:00.789 WARN  MafOutputRenderer - 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=
15:09:00.790 WARN  MafOutputRenderer - 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=
15:09:00.791 WARN  MafOutputRenderer - 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=
15:09:00.791 WARN  MafOutputRenderer - 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=
15:09:00.791 WARN  MafOutputRenderer - 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=
15:09:00.792 WARN  MafOutputRenderer - 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=
15:09:00.792 WARN  MafOutputRenderer - 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=
15:09:00.793 WARN  MafOutputRenderer - 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=
15:09:00.793 WARN  MafOutputRenderer - 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=
15:09:00.793 WARN  MafOutputRenderer - 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=
15:09:00.794 WARN  MafOutputRenderer - 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=
15:09:00.795 WARN  MafOutputRenderer - 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=
15:09:00.795 WARN  MafOutputRenderer - 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=
15:09:00.796 WARN  MafOutputRenderer - 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=
15:09:00.796 WARN  MafOutputRenderer - 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=
15:09:00.797 WARN  MafOutputRenderer - 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=
15:09:00.797 WARN  MafOutputRenderer - 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=
15:09:00.797 WARN  MafOutputRenderer - 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=
15:09:00.798 WARN  MafOutputRenderer - 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=
15:09:00.799 WARN  MafOutputRenderer - 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=
15:09:00.800 WARN  MafOutputRenderer - 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=
15:09:00.800 WARN  MafOutputRenderer - 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=
15:09:00.801 WARN  MafOutputRenderer - 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=
15:09:00.802 WARN  MafOutputRenderer - 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=
15:09:00.802 WARN  MafOutputRenderer - 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=
15:09:00.803 WARN  MafOutputRenderer - 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=
15:09:00.804 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTA] attr={} GT=[] filters=
15:09:00.804 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
15:09:00.804 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, AT] attr={} GT=[] filters=
15:09:00.805 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TT] attr={} GT=[] filters=
15:09:00.806 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CT] attr={} GT=[] filters=
15:09:00.806 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
15:09:00.806 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916622 Q40.00 of type=INDEL alleles=[A*, ATATT] attr={} GT=[] filters=
15:09:00.808 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619 Q40.00 of type=INDEL alleles=[T*, TTATT] attr={} GT=[] filters=
15:09:00.808 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620 Q40.00 of type=INDEL alleles=[C*, CTATT] attr={} GT=[] filters=
15:09:00.809 WARN  MafOutputRenderer - 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=
15:09:00.809 WARN  MafOutputRenderer - 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=
15:09:00.810 WARN  MafOutputRenderer - 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=
15:09:00.810 WARN  MafOutputRenderer - 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=
15:09:00.811 WARN  MafOutputRenderer - 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=
15:09:00.812 WARN  MafOutputRenderer - 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=
15:09:00.812 WARN  MafOutputRenderer - 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=
15:09:00.812 WARN  MafOutputRenderer - 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=
15:09:00.813 WARN  MafOutputRenderer - 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=
15:09:00.814 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916620 Q40.00 of type=INDEL alleles=[TC*, T] attr={} GT=[] filters=
15:09:00.814 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916621 Q40.00 of type=INDEL alleles=[CC*, C] attr={} GT=[] filters=
15:09:00.814 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916622 Q40.00 of type=INDEL alleles=[CA*, C] attr={} GT=[] filters=
15:09:00.815 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916622 Q40.00 of type=INDEL alleles=[CTCCA*, C] attr={} GT=[] filters=
15:09:00.816 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916623 Q40.00 of type=INDEL alleles=[TCCAC*, T] attr={} GT=[] filters=
15:09:00.816 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916624 Q40.00 of type=INDEL alleles=[CCACG*, C] attr={} GT=[] filters=
15:09:00.816 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916625 Q40.00 of type=INDEL alleles=[CACGA*, C] attr={} GT=[] filters=
15:09:00.818 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916618-178916625 Q40.00 of type=INDEL alleles=[CTCCACGA*, C] attr={} GT=[] filters=
15:09:00.818 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916619-178916626 Q40.00 of type=INDEL alleles=[TCCACGAC*, T] attr={} GT=[] filters=
15:09:00.818 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916620-178916627 Q40.00 of type=INDEL alleles=[CCACGACC*, C] attr={} GT=[] filters=
15:09:00.819 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ chr3:178916621-178916628 Q40.00 of type=INDEL alleles=[CACGACCA*, C] attr={} GT=[] filters=
15:09:00.819 INFO  ProgressMeter -             unmapped              0.0                    57         103636.4
15:09:00.819 INFO  ProgressMeter - Traversal complete. Processed 57 total variants in 0.0 minutes.
15:09:00.819 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/1
15:09:00.819 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:09:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:09:00.820 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out12781114202615861897.vcf
15:09:00.934 INFO  Funcotator - ------------------------------------------------------------
15:09:00.934 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:09:00.934 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:00.934 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:09:00.934 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:00.934 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:09:00 PM GMT
15:09:00.934 INFO  Funcotator - ------------------------------------------------------------
15:09:00.934 INFO  Funcotator - ------------------------------------------------------------
15:09:00.934 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:09:00.934 INFO  Funcotator - Picard Version: 3.4.0
15:09:00.934 INFO  Funcotator - Built for Spark Version: 3.5.0
15:09:00.934 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:00.934 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:00.934 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:00.934 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:00.934 INFO  Funcotator - Deflater: IntelDeflater
15:09:00.934 INFO  Funcotator - Inflater: IntelInflater
15:09:00.934 INFO  Funcotator - GCS max retries/reopens: 20
15:09:00.934 INFO  Funcotator - Requester pays: disabled
15:09:00.934 INFO  Funcotator - Initializing engine
15:09:00.935 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/0816201804HC0_R01C01.pik3ca.vcf
15:09:00.936 INFO  Funcotator - Done initializing engine
15:09:00.936 INFO  Funcotator - Skipping sequence dictionary validation.
15:09:00.936 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:09:00.936 INFO  Funcotator - Initializing data sources...
15:09:00.936 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_pik3ca/
15:09:00.936 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:09:00.937 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
15:09:00.937 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
15:09:00.937 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
15:09:00.937 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:09:00.937 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
15:09:00.937 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:09:00.938 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
15:09:00.938 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
15:09:00.938 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
15:09:00.938 INFO  DataSourceUtils - Setting lookahead cache for data source: dummy_ClinVar_VCF : 100000
15:09:00.939 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
15:09:00.939 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
15:09:00.940 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
15:09:00.941 INFO  Funcotator - Initializing Funcotator Engine...
15:09:00.941 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:09:00.941 WARN  FuncotatorEngine - WARNING: You are using B37 as a reference.  Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases.  There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
15:09:00.941 INFO  Funcotator - Creating a MAF file for output: file:/tmp/funcotator_tmp_out12429295326649377560.maf
15:09:00.942 INFO  ProgressMeter - Starting traversal
15:09:00.942 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:00.944 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.945 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.945 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.946 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.947 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.947 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.947 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.948 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.948 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.949 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.949 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.949 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.949 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.950 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.950 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.950 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.951 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.951 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.951 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.951 WARN  MafOutputRenderer - No dbSNP annotations exist for this variant.  Cannot render the dbSNP fields in the MAF.  These fields will not be correct.  [VC Unknown @ 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=
15:09:00.951 INFO  ProgressMeter -             unmapped              0.0                    21         140000.0
15:09:00.952 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:09:00.952 INFO  VcfFuncotationFactory - dummy_ClinVar_VCF 20180401 cache hits/total: 0/4
15:09:00.952 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:09:00 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:09:01.043 INFO  Funcotator - ------------------------------------------------------------
15:09:01.043 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:09:01.043 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:01.043 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:09:01.043 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:01.043 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:09:01 PM GMT
15:09:01.043 INFO  Funcotator - ------------------------------------------------------------
15:09:01.043 INFO  Funcotator - ------------------------------------------------------------
15:09:01.043 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:09:01.043 INFO  Funcotator - Picard Version: 3.4.0
15:09:01.043 INFO  Funcotator - Built for Spark Version: 3.5.0
15:09:01.043 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:01.043 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:01.043 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:01.043 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:01.043 INFO  Funcotator - Deflater: IntelDeflater
15:09:01.043 INFO  Funcotator - Inflater: IntelInflater
15:09:01.043 INFO  Funcotator - GCS max retries/reopens: 20
15:09:01.043 INFO  Funcotator - Requester pays: disabled
15:09:01.043 INFO  Funcotator - Initializing engine
15:09:01.044 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_column_test.vcf
15:09:01.045 INFO  Funcotator - Done initializing engine
15:09:01.045 INFO  Funcotator - Skipping sequence dictionary validation.
15:09:01.045 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:09:01.045 INFO  Funcotator - Initializing data sources...
15:09:01.045 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
15:09:01.045 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:09:01.045 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
15:09:01.045 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
15:09:01.045 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
15:09:01.045 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:09:01.045 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:09:01.046 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
15:09:01.046 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
15:09:01.073 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
15:09:01.073 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 15:09:01	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:09:01.074 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
15:09:01.074 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:09:01.075 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
15:09:01.075 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
15:09:01.075 INFO  Funcotator - Initializing Funcotator Engine...
15:09:01.075 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:09:01.075 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.
15:09:01.075 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12529743162475626449.vcf
15:09:01.079 INFO  ProgressMeter - Starting traversal
15:09:01.079 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:01.082 INFO  ProgressMeter -             unmapped              0.0                    10         200000.0
15:09:01.082 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
15:09:01.082 WARN  Funcotator - ================================================================================
15:09:01.082 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:09:01.082 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:09:01.082 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:09:01.082 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:09:01.082 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:09:01.082 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:09:01.082 WARN  Funcotator - --------------------------------------------------------------------------------
15:09:01.082 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:09:01.082 WARN  Funcotator -  run was misconfigured.     
15:09:01.082 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:09:01.082 WARN  Funcotator - ================================================================================
15:09:01.083 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:09:01 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:09:01.084 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out12529743162475626449.vcf
15:09:01.177 INFO  Funcotator - ------------------------------------------------------------
15:09:01.177 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:09:01.177 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:01.177 INFO  Funcotator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:09:01.177 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:01.177 INFO  Funcotator - Start Date/Time: May 27, 2025 at 3:09:01 PM GMT
15:09:01.177 INFO  Funcotator - ------------------------------------------------------------
15:09:01.177 INFO  Funcotator - ------------------------------------------------------------
15:09:01.177 INFO  Funcotator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:09:01.177 INFO  Funcotator - Picard Version: 3.4.0
15:09:01.177 INFO  Funcotator - Built for Spark Version: 3.5.0
15:09:01.177 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:01.177 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:01.177 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:01.177 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:01.177 INFO  Funcotator - Deflater: IntelDeflater
15:09:01.177 INFO  Funcotator - Inflater: IntelInflater
15:09:01.177 INFO  Funcotator - GCS max retries/reopens: 20
15:09:01.177 INFO  Funcotator - Requester pays: disabled
15:09:01.177 INFO  Funcotator - Initializing engine
15:09:01.178 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/clinvar_hg19_multihit_test.vcf
15:09:01.179 INFO  Funcotator - Done initializing engine
15:09:01.179 INFO  Funcotator - Skipping sequence dictionary validation.
15:09:01.179 INFO  Funcotator - Processing user transcripts/defaults/overrides...
15:09:01.179 INFO  Funcotator - Initializing data sources...
15:09:01.179 INFO  DataSourceUtils - Initializing data sources from directory: /gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/
15:09:01.179 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
15:09:01.179 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
15:09:01.180 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
15:09:01.180 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
15:09:01.180 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
15:09:01.180 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
15:09:01.180 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
15:09:01.180 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/funcotator/small_ds_clinvar_hg19/clinvar/hg19/clinvar_hgmd.config
15:09:01.208 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
15:09:01.209 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 15:09:01	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:09:01.209 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
15:09:01.209 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
15:09:01.210 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
15:09:01.210 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
15:09:01.210 INFO  Funcotator - Initializing Funcotator Engine...
15:09:01.210 INFO  FuncotatorEngine - Forcing B37 -> HG19 Variant conversion.
15:09:01.210 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.
15:09:01.210 INFO  Funcotator - Creating a VCF file for output: file:/tmp/funcotator_tmp_out12346848711391733326.vcf
15:09:01.213 INFO  ProgressMeter - Starting traversal
15:09:01.213 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:01.215 INFO  ProgressMeter -             unmapped              0.0                     1          30000.0
15:09:01.215 INFO  ProgressMeter - Traversal complete. Processed 1 total variants in 0.0 minutes.
15:09:01.215 WARN  Funcotator - ================================================================================
15:09:01.215 WARN  Funcotator - ?[43m     _  _  _   __        __               _                   _  _  _           
15:09:01.215 WARN  Funcotator -     | || || |  \ \      / /_ _ _ __ _ __ (_)_ __   __ _      | || || |        
15:09:01.215 WARN  Funcotator -     | || || |   \ \ /\ / / _` | '__| '_ \| | '_ \ / _` |     | || || |     
15:09:01.215 WARN  Funcotator -     |_||_||_|    \ \V V / (_| | |  | | | | | | | | (_| |     |_||_||_|        
15:09:01.215 WARN  Funcotator -     (_)(_)(_)     \_/\_/ \__,_|_|  |_| |_|_|_| |_|\__, |     (_)(_)(_)      
15:09:01.215 WARN  Funcotator -                                                   |___/                         ?[0;0m
15:09:01.215 WARN  Funcotator - --------------------------------------------------------------------------------
15:09:01.215 WARN  Funcotator -  Only IGRs were produced for this dataset.  This STRONGLY indicates that this   
15:09:01.215 WARN  Funcotator -  run was misconfigured.     
15:09:01.215 WARN  Funcotator -  You MUST check your data sources to make sure they are correct for these data.
15:09:01.215 WARN  Funcotator - ================================================================================
15:09:01.216 INFO  Funcotator - Shutting down engine
[May 27, 2025 at 3:09:01 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2973761536
15:09:01.217 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/funcotator_tmp_out12346848711391733326.vcf