Class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.varianteval > VariantEvalIntegrationTest
45

tests
0

failures
0

ignored
16.180s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.112s passed
testAlleleCountStratWithMLE 0.102s passed
testBadACValue 0.065s passed
testCompOverlap 0.134s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.320s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.257s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.273s passed
testEvalTrackWithoutGenotypes 0.365s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.091s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.071s passed
testFunctionClassWithSnpeff 0.656s passed
testFundamentalsCountVariantsNoCompRod 0.074s passed
testFundamentalsCountVariantsSNPsAndIndels 0.083s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.126s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.085s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.083s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.116s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.084s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.080s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.082s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.077s passed
testIncompatibleEvalAndStrat 0.068s passed
testIntervalStrat 0.073s passed
testMVEvalFamilyStrat 0.082s passed
testModernVCFWithLargeIndels 0.433s passed
testMultipleCompTracks 0.254s passed
testMultipleEvalTracksAlleleCountWithMerge 0.120s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.097s passed
testMultipleEvalTracksWithoutGenotypes 0.426s passed
testOutputFileCreation 0.114s passed
testPedigreeValidation[0](SILENT, false) 0.078s passed
testPedigreeValidation[1](STRICT, true) 0.072s passed
testPedigreeValidation[2](null, true) 0.066s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.154s passed
testPrintMissingComp 0.095s passed
testSelect1 9.066s passed
testStandardIndelEval 0.769s passed
testStratifySamplesAndExcludeMonomorphicSites 0.350s passed
testVEMendelianViolationEvaluator 0.079s passed
testValidationReport[0](sites-sites, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportEval.noGenotypes.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportComp.noGenotypes.vcf) 0.073s passed
testValidationReport[1](sites-genotypes, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportEval.noGenotypes.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportComp.vcf) 0.071s passed
testValidationReport[2](genotypes-sites, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportEval.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportComp.noGenotypes.vcf) 0.070s passed
testValidationReport[3](genotypes-genotypes, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportEval.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportComp.vcf) 0.072s passed
testWithAC0 0.087s passed
testWithoutAC0 0.075s passed

Standard output

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[19:09:23] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[19:09:23] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[19:09:23] Executing test VariantEvalIntegrationTest:testBadACValue
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[19:09:23] Executing test VariantEvalIntegrationTest:testCompOverlap
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[19:09:23] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[19:09:23] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[19:09:24] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[19:09:24] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[19:09:24] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[19:09:24] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[19:09:24] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[19:09:25] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[19:09:25] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[19:09:25] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[19:09:25] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[19:09:25] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[19:09:26] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[19:09:26] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[19:09:26] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[19:09:26] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[19:09:26] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[19:09:26] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[19:09:26] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[19:09:26] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[19:09:26] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[19:09:27] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[19:09:27] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[19:09:27] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[19:09:27] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[19:09:28] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[19:09:28] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[19:09:28] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[19:09:28] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[19:09:28] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[19:09:28] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[19:09:28] Executing test VariantEvalIntegrationTest:testSelect1
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[19:09:37] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[19:09:38] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[19:09:38] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[19:09:38] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[19:09:38] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[19:09:39] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[19:09:39] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[19:09:39] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[19:09:39] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 19, 2025 at 7:09:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528