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

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

tests

failures

ignored

12.893s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testASAnnotationsAndSubsetting	3.514s	passed
testAddedHcAsAnnotations	0.153s	passed
testAggressiveQualFiltering	0.127s	passed
testContiguityWithSpanningDels	0.399s	passed
testDragenGvcfs	0.214s	passed
testFilters	0.219s	passed
testFirstPositionOnContigNotDropped	0.152s	passed
testGVCFReblockingIsContiguous	4.311s	passed
testHomRefCalls	0.160s	passed
testLeftContigBoundary	0.152s	passed
testMQHeadersAreUpdated	0.198s	passed
testMixedSamples	0.164s	passed
testMovingFilters	0.219s	passed
testMultipleInputs	0.339s	passed
testNewCompressionScheme	0.111s	passed
testNoCallGenotypes	0.154s	passed
testNoCallWhenGQ0InNonRefAllele	0.156s	passed
testNonGVCFInput	0.099s	passed
testNonRefADCorrection	0.098s	passed
testOneSampleAsForGnomAD	0.103s	passed
testOverlappingDeletions	0.252s	passed
testPosteriorDisagreementNeedingSubset	0.156s	passed
testRawMQInput	0.127s	passed
testReReblocking	0.217s	passed
testRemovingAnnotationFromEmptyAttributes	0.158s	passed
testRemovingFormatAnnotations	0.198s	passed
testSpanDelRegression	0.105s	passed
testTreeScoreThreshold	0.106s	passed
testTreeScoreWithNoAnnotation	0.103s	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, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)	0.104s	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 , /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz)	0.170s	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 , /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz)	0.155s	passed

Standard output

--------------------------------------------------------------------------------
[15:22:30] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[15:22:30] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[15:22:34] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[15:22:41] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[15:22:41] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[15:22:41] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[15:22:41] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[15:22:42] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[15:22:43] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[15:22:43] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
--------------------------------------------------------------------------------
[15:22:43] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 27, 2025 at 3:22:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:39 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:39 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000