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

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

tests

failures

ignored

12.554s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testASAnnotationsAndSubsetting	2.962s	passed
testAddedHcAsAnnotations	0.152s	passed
testAggressiveQualFiltering	0.139s	passed
testContiguityWithSpanningDels	0.429s	passed
testDragenGvcfs	0.220s	passed
testFilters	0.219s	passed
testFirstPositionOnContigNotDropped	0.158s	passed
testGVCFReblockingIsContiguous	4.474s	passed
testHomRefCalls	0.160s	passed
testLeftContigBoundary	0.158s	passed
testMQHeadersAreUpdated	0.205s	passed
testMixedSamples	0.164s	passed
testMovingFilters	0.222s	passed
testMultipleInputs	0.341s	passed
testNewCompressionScheme	0.109s	passed
testNoCallGenotypes	0.157s	passed
testNoCallWhenGQ0InNonRefAllele	0.154s	passed
testNonGVCFInput	0.099s	passed
testNonRefADCorrection	0.111s	passed
testOneSampleAsForGnomAD	0.099s	passed
testOverlappingDeletions	0.258s	passed
testPosteriorDisagreementNeedingSubset	0.153s	passed
testRawMQInput	0.122s	passed
testReReblocking	0.215s	passed
testRemovingAnnotationFromEmptyAttributes	0.155s	passed
testRemovingFormatAnnotations	0.198s	passed
testSpanDelRegression	0.106s	passed
testTreeScoreThreshold	0.098s	passed
testTreeScoreWithNoAnnotation	0.098s	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)	0.103s	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)	0.164s	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)	0.152s	passed

Standard output

--------------------------------------------------------------------------------
[19:24:21] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[19:24:21] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[19:24:24] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[19:24:31] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[19:24:31] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[19:24:32] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[19:24:32] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[19:24:32] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[19:24:33] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[19:24:33] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
--------------------------------------------------------------------------------
[19:24:33] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 19, 2025 at 7:24:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000