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

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

tests
0

failures
0

ignored
17.455s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.375s passed
testAlleleCountStratWithMLE 0.118s passed
testBadACValue 0.085s passed
testCompOverlap 0.154s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.309s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.376s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.406s passed
testEvalTrackWithoutGenotypes 0.521s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.154s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.103s passed
testFunctionClassWithSnpeff 0.695s passed
testFundamentalsCountVariantsNoCompRod 0.087s passed
testFundamentalsCountVariantsSNPsAndIndels 0.096s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.129s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.097s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.098s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.116s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.088s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.091s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.093s passed
testIncompatibleEvalAndStrat 0.079s passed
testIntervalStrat 0.081s passed
testMVEvalFamilyStrat 0.093s passed
testModernVCFWithLargeIndels 0.718s passed
testMultipleCompTracks 0.391s passed
testMultipleEvalTracksAlleleCountWithMerge 0.142s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.088s passed
testMultipleEvalTracksWithoutGenotypes 0.409s passed
testOutputFileCreation 0.112s passed
testPedigreeValidation[0](SILENT, false) 0.090s passed
testPedigreeValidation[1](STRICT, true) 0.081s passed
testPedigreeValidation[2](null, true) 0.076s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.170s passed
testPrintMissingComp 0.098s passed
testSelect1 8.915s passed
testStandardIndelEval 0.695s passed
testStratifySamplesAndExcludeMonomorphicSites 0.366s passed
testVEMendelianViolationEvaluator 0.086s 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) 0.093s 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) 0.075s 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) 0.074s 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) 0.077s passed
testWithAC0 0.089s passed
testWithoutAC0 0.079s passed

Standard output

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[14:45:52] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[14:45:53] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[14:45:53] Executing test VariantEvalIntegrationTest:testBadACValue
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[14:45:53] Executing test VariantEvalIntegrationTest:testCompOverlap
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[14:45:53] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[14:45:53] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[14:45:54] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[14:45:54] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[14:45:55] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[14:45:55] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[14:45:55] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[14:45:56] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[14:45:56] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[14:45:56] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[14:45:56] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[14:45:56] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[14:45:56] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[14:45:56] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[14:45:56] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[14:45:56] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[14:45:56] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[14:45:57] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[14:45:57] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[14:45:57] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[14:45:57] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[14:45:58] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[14:45:58] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[14:45:58] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[14:45:58] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[14:45:59] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[14:45:59] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[14:45:59] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[14:45:59] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[14:45:59] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[14:45:59] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[14:45:59] Executing test VariantEvalIntegrationTest:testSelect1
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[14:46:08] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[14:46:09] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[14:46:09] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[14:46:09] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[14:46:09] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[14:46:09] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[14:46:10] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[14:46:10] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[14:46:10] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[June 2, 2025 at 2:45:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:45:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000