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

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

tests
0

failures
0

ignored
12.481s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.901s passed
testAddedHcAsAnnotations 0.127s passed
testAggressiveQualFiltering 0.080s passed
testContiguityWithSpanningDels 0.370s passed
testDragenGvcfs 0.204s passed
testFilters 0.199s passed
testFirstPositionOnContigNotDropped 0.131s passed
testGVCFReblockingIsContiguous 4.262s passed
testHomRefCalls 0.138s passed
testLeftContigBoundary 0.130s passed
testMQHeadersAreUpdated 0.185s passed
testMixedSamples 0.145s passed
testMovingFilters 0.213s passed
testMultipleInputs 0.291s passed
testNewCompressionScheme 0.083s passed
testNoCallGenotypes 0.136s passed
testNoCallWhenGQ0InNonRefAllele 0.131s passed
testNonGVCFInput 0.078s passed
testNonRefADCorrection 0.073s passed
testOneSampleAsForGnomAD 0.073s passed
testOverlappingDeletions 0.210s passed
testPosteriorDisagreementNeedingSubset 0.130s passed
testRawMQInput 0.098s passed
testReReblocking 0.199s passed
testRemovingAnnotationFromEmptyAttributes 0.129s passed
testRemovingFormatAnnotations 0.193s passed
testSpanDelRegression 0.081s passed
testTreeScoreThreshold 0.076s passed
testTreeScoreWithNoAnnotation 0.073s 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) 0.074s 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) 0.139s 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) 0.129s passed

Standard output

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[15:55:04] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[15:55:05] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[15:55:08] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[15:55:15] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[15:55:15] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[15:55:15] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[15:55:15] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[15:55:16] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[15:55:17] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[15:55:17] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[15:55:17] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 19, 2025 at 3:55:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:08 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:08 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:08 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848