Class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCFIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.variantutils > ReblockGVCFIntegrationTest
32

tests
0

failures
0

ignored
12.796s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.922s passed
testAddedHcAsAnnotations 0.143s passed
testAggressiveQualFiltering 0.106s passed
testContiguityWithSpanningDels 0.402s passed
testDragenGvcfs 0.191s passed
testFilters 0.199s passed
testFirstPositionOnContigNotDropped 0.129s passed
testGVCFReblockingIsContiguous 4.439s passed
testHomRefCalls 0.186s passed
testLeftContigBoundary 0.143s passed
testMQHeadersAreUpdated 0.183s passed
testMixedSamples 0.136s passed
testMovingFilters 0.192s passed
testMultipleInputs 0.290s passed
testNewCompressionScheme 0.083s passed
testNoCallGenotypes 0.133s passed
testNoCallWhenGQ0InNonRefAllele 0.125s passed
testNonGVCFInput 0.076s passed
testNonRefADCorrection 0.081s passed
testOneSampleAsForGnomAD 0.077s passed
testOverlappingDeletions 0.203s passed
testPosteriorDisagreementNeedingSubset 0.129s passed
testRawMQInput 0.104s passed
testReReblocking 0.208s passed
testRemovingAnnotationFromEmptyAttributes 0.140s passed
testRemovingFormatAnnotations 0.179s passed
testSpanDelRegression 0.087s passed
testTreeScoreThreshold 0.078s passed
testTreeScoreWithNoAnnotation 0.074s passed
testWithExactComparison[0](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/gvcfForReblocking.g.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testJustOneSample.expected.g.vcf, -L chr20:69771 -rgq-threshold 19, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta) 0.080s passed
testWithExactComparison[1](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWgsInput.g.vcf , src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWgsOutput.g.vcf, -do-qual-approx --floor-blocks -GQB 20 -GQB 30 -GQB 40 , /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz) 0.142s passed
testWithExactComparison[2](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWesInput.g.vcf , src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWesOutput.g.vcf, -do-qual-approx --floor-blocks -GQB 20 -GQB 30 -GQB 40 , /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz) 0.136s passed

Standard output

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[14:00:01] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[14:00:01] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[14:00:05] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[14:00:12] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[14:00:12] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[14:00:12] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[14:00:12] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[14:00:12] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[14:00:13] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[14:00:13] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[14:00:14] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 27, 2025 at 2:00:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:06 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:06 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:06 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 2:00:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464