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

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

tests
0

failures
0

ignored
12.461s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.273s passed
testAddedHcAsAnnotations 0.120s passed
testAggressiveQualFiltering 0.081s passed
testContiguityWithSpanningDels 0.393s passed
testDragenGvcfs 0.191s passed
testFilters 0.201s passed
testFirstPositionOnContigNotDropped 0.128s passed
testGVCFReblockingIsContiguous 4.851s passed
testHomRefCalls 0.202s passed
testLeftContigBoundary 0.129s passed
testMQHeadersAreUpdated 0.179s passed
testMixedSamples 0.143s passed
testMovingFilters 0.199s passed
testMultipleInputs 0.281s passed
testNewCompressionScheme 0.084s passed
testNoCallGenotypes 0.134s passed
testNoCallWhenGQ0InNonRefAllele 0.131s passed
testNonGVCFInput 0.076s passed
testNonRefADCorrection 0.074s passed
testOneSampleAsForGnomAD 0.075s passed
testOverlappingDeletions 0.210s passed
testPosteriorDisagreementNeedingSubset 0.137s passed
testRawMQInput 0.104s passed
testReReblocking 0.194s passed
testRemovingAnnotationFromEmptyAttributes 0.127s passed
testRemovingFormatAnnotations 0.170s passed
testSpanDelRegression 0.076s passed
testTreeScoreThreshold 0.078s passed
testTreeScoreWithNoAnnotation 0.075s 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) 0.075s 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) 0.143s 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) 0.127s passed

Standard output

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[15:55:40] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[15:55:40] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[15:55:44] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[15:55:51] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[15:55:51] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[15:55:51] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[15:55:51] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[15:55:52] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[15:55:52] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[15:55:52] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[15:55:53] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 27, 2025 at 3:55:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432