Class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariantsIntegrationTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testAlleleTrimming | 0.072s | passed |
| testCombineInfoAndGenotypeJexl | 0.077s | passed |
| testComplexSelection | 0.074s | passed |
| testComplexSelectionWithNonExistingSamples | 0.072s | passed |
| testConcordance | 0.074s | passed |
| testDiscordance | 0.072s | passed |
| testDropAnnotations[0](-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894, testSelectVariants_DropAnnotations.vcf, standard) | 0.073s | passed |
| testDropAnnotations[1](-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894 -DA NotAnAnnotation -DGA AlsoNotAnAnnotation, testSelectVariants_DropAnnotations.vcf, unused_annotations) | 0.072s | passed |
| testDropAnnotations[2](-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894 -select 'FisherStrand > 10.0', testSelectVariants_DropAnnotationsSelectFisherStrand.vcf, select_on_dropped_annotation) | 0.071s | passed |
| testDropAnnotations[3](-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894 -select 'RMSMAPQ > 175.0', testSelectVariants_DropAnnotationsSelectRMSMAPQ.vcf, select_on_kept_annotation) | 0.072s | passed |
| testDropAnnotations[4](-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894 -select 'vc.getGenotype("NA11894").getExtendedAttribute("RD")>6', testSelectVariants_DropAnnotationsSelectRD.vcf, select_on_dropped_genotype_annotation) | 0.076s | passed |
| testDropAnnotations[5](-DA FisherStrand -DA OnOffGenotype -DGA RD -sn NA11894 -select 'vc.getGenotype("NA11894").getGQ()==1', testSelectVariants_DropAnnotationsSelectGQ.vcf, select_on_kept_genotype_annotation) | 0.075s | passed |
| testEmptyVcfException | 0.068s | passed |
| testExcludeSelectionIDFromFile | 0.075s | passed |
| testExcludeSelectionIDLiteral | 0.072s | passed |
| testExcludeSelectionType | 0.075s | passed |
| testExpressionSelection | 0.074s | passed |
| testFORMATFieldGivenToSelect | 0.072s | passed |
| testFileWithoutInfoLineInHeader | 0.072s | passed |
| testFileWithoutInfoLineInHeaderWithOverride | 0.071s | passed |
| testHaploid | 0.076s | passed |
| testINFOFieldGivenToSelectGenotype | 0.076s | passed |
| testInvalidJexl | 0.072s | passed |
| testInvertJexlSelection | 0.075s | passed |
| testInvertMendelianViolationSelection | 0.076s | passed |
| testInvertSelection | 0.073s | passed |
| testJEXLFilterFirst | 0.145s | passed |
| testJexlDirectlyAccessGenotype | 0.072s | passed |
| testJexlGenotypeFilter | 0.072s | passed |
| testKeepOriginalAC | 0.068s | passed |
| testKeepOriginalACAndENV | 0.069s | passed |
| testKeepOriginalDP | 0.077s | passed |
| testKeepSelectionIDFromFile | 0.069s | passed |
| testKeepSelectionIDLiteral | 0.071s | passed |
| testLogicalAndOrInJexl | 0.073s | passed |
| testManyAllelicWithoutPLsDoesntFreeze | 0.079s | passed |
| testMaxFilteredGenotypesSelection | 0.071s | passed |
| testMaxFractionFilteredGenotypesSelection | 0.073s | passed |
| testMaxIndelLengthSelection | 0.069s | passed |
| testMaxNoCall0_25 | 0.069s | passed |
| testMaxNoCall0_5 | 0.068s | passed |
| testMaxNoCall1 | 0.069s | passed |
| testMaxNoCall2 | 0.070s | passed |
| testMendelianViolationSelection | 0.074s | passed |
| testMinFilteredGenotypesSelection | 0.068s | passed |
| testMinFractionFilteredGenotypesSelection | 0.070s | passed |
| testMinIndelLengthSelection | 0.069s | passed |
| testMissingVcfException | 0.067s | passed |
| testMultiAllelicAnnotationOrdering | 0.072s | passed |
| testMultipleINFOJexls | 0.071s | passed |
| testMultipleRecordsAtOnePosition | 0.070s | passed |
| testNoGTs | 0.068s | passed |
| testNonExistentSampleFile | 0.064s | passed |
| testNonExistingFieldSelection | 0.070s | passed |
| testNotFileVcfException | 0.067s | passed |
| testOutputOnlyStartingInInterval | 0.072s | passed |
| testRemoveMLE | 0.068s | passed |
| testRemoveSingleSpanDelAllele | 0.070s | passed |
| testRemoveSingleSpanDelAlleleExNonVar | 0.074s | passed |
| testRemoveSingleSpanDelAlleleNoSpanDel | 0.073s | passed |
| testRepeatedLineSelectionAndExludeFiltered | 0.083s | passed |
| testResortingFileWarning | 0.074s | passed |
| testSACDiploid | 0.082s | passed |
| testSACNonDiploid | 0.082s | passed |
| testSACSimpleDiploid | 0.071s | passed |
| testSampleExclusionFromFileAndSeparateSample | 0.073s | passed |
| testSampleExclusionJustFromExpression | 0.075s | passed |
| testSampleExclusionJustFromFile | 0.073s | passed |
| testSampleExclusionJustFromNegationExpression | 0.073s | passed |
| testSampleInclusionWithNonexistingSamples | 0.069s | passed |
| testSampleSelection | 0.073s | passed |
| testSelectFromMultiAllelic | 0.090s | passed |
| testSelectRandomFraction | 0.076s | passed |
| testSetFilteredGtoNocall | 0.071s | passed |
| testSetFilteredGtoNocallUpdateInfo | 0.072s | passed |
| testTetraDiploid | 0.072s | passed |
| testTetraploid | 0.074s | passed |
| testUntrimmedVariants | 0.070s | passed |
| testUntrimmedVariantsWithSetFilteredGtToNocall | 0.069s | passed |
| testUnusedAlleleTrimming[0](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/forHardLeftAlignVariantsTest.vcf, --remove-unused-alternates, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_UnusedAlleleHardLeftTrim.vcf) | 0.069s | passed |
| testUnusedAlleleTrimming[1](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/forHardLeftAlignVariantsTest.vcf, null, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_UnusedAlleleHardLeft.vcf) | 0.069s | passed |
| testUnusedAlleleTrimming[2](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/multi-allelic-ordering.vcf, -sn SAMPLE-CC -sn SAMPLE-CT, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_UnusedAlleleCCCT.vcf) | 0.072s | passed |
| testUnusedAlleleTrimming[3](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/multi-allelic-ordering.vcf, -sn SAMPLE-CC -sn SAMPLE-CT --exclude-non-variants, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_UnusedAlleleCCCTEnv.vcf) | 0.072s | passed |
| testUnusedAlleleTrimming[4](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/multi-allelic-ordering.vcf, -sn SAMPLE-CC -sn SAMPLE-CT --remove-unused-alternates, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_UnusedAlleleCCCTTrim.vcf) | 0.073s | passed |
| testUnusedAlleleTrimming[5](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/multi-allelic-ordering.vcf, -sn SAMPLE-CC -sn SAMPLE-CT --exclude-non-variants --remove-unused-alternates, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_UnusedAlleleCCCTTrimAltEnv.vcf) | 0.071s | passed |
| testUseCorrectDPInJexl | 0.151s | passed |
| testVariantTypeSelection | 0.074s | passed |
| testVariantTypeSelectionForGVCF | 0.069s | passed |
Standard output
-------------------------------------------------------------------------------- [15:55:17] Executing test SelectVariantsIntegrationTest:testAlleleTrimming -------------------------------------------------------------------------------- [15:55:17] Executing test SelectVariantsIntegrationTest:testComplexSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:17] Executing test SelectVariantsIntegrationTest:testComplexSelectionWithNonExistingSamples--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:17] Executing test SelectVariantsIntegrationTest:testConcordance--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:17] Executing test SelectVariantsIntegrationTest:testDiscordance--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:17] Executing test SelectVariantsIntegrationTest:testDropAnnotations--standard -------------------------------------------------------------------------------- [15:55:17] Executing test SelectVariantsIntegrationTest:testDropAnnotations--unused_annotations -------------------------------------------------------------------------------- [15:55:17] Executing test SelectVariantsIntegrationTest:testDropAnnotations--select_on_dropped_annotation -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:testDropAnnotations--select_on_kept_annotation -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:testDropAnnotations--select_on_dropped_genotype_annotation -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:testDropAnnotations--select_on_kept_genotype_annotation -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:testEmptyVcfException--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/reallyEmpty.vcf -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:testExcludeSelectionIDFile--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/complexExample1.vcf -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:testExcludeSelectionIDLiteral--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/complexExample1.vcf -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:testExcludeSelectionType--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/complexExample1.vcf -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:testSimpleExpressionSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/filteringDepthInFormat.vcf -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:testSelectVariants_FileWithoutInfoLineInHeader -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:testSelectVariants_FileWithoutInfoLineInHeaderWithOverride -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:testHaploid--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/haploid-multisample.vcf -------------------------------------------------------------------------------- [15:55:18] Executing test SelectVariantsIntegrationTest:InvalidJexl -------------------------------------------------------------------------------- [15:55:19] Executing test SelectVariantsIntegrationTest:testInvertJexlSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:19] Executing test SelectVariantsIntegrationTest:testInvertMendelianViolationSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/CEUtrioTest.vcf -------------------------------------------------------------------------------- [15:55:19] Executing test SelectVariantsIntegrationTest:testInvertSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:19] Executing test SelectVariantsIntegrationTest:testKeepOriginalAC--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample.loseAlleleInSelection.vcf -------------------------------------------------------------------------------- [15:55:19] Executing test SelectVariantsIntegrationTest:testKeepOriginalACAndENV--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample.loseAlleleInSelection.vcf -------------------------------------------------------------------------------- [15:55:19] Executing test SelectVariantsIntegrationTest:testKeepOriginalDP--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/CEUtrioTest.vcf -------------------------------------------------------------------------------- [15:55:19] Executing test SelectVariantsIntegrationTest:testKeepSelectionIDFile--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/complexExample1.vcf -------------------------------------------------------------------------------- [15:55:19] Executing test SelectVariantsIntegrationTest:testKeepSelectionIDLiteral--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/complexExample1.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMaxFilteredGenotypesSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/filteredSamples.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMaxFractionFilteredGenotypesSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/filteredSamples.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMaxIndelLengthSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/complexExample1.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMaxNoCall0_25--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample.forNoCallFiltering.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMaxNoCall0_5--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample.forNoCallFiltering.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMaxNoCall1--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample.forNoCallFiltering.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMaxNoCall2--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample.forNoCallFiltering.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMendelianViolationSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/CEUtrioTest.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMinFilteredGenotypesSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/filteredSamples.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMinFractionFilteredGenotypesSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/filteredSamples.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMinIndelLengthSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/complexExample1.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:testMissingVcfException--test.vcf -------------------------------------------------------------------------------- [15:55:20] Executing test SelectVariantsIntegrationTest:test multi allelic annotation ordering --src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/multi-allelic-ordering.vcf -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:testMultipleRecordsAtOnePosition--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/selectVariants.onePosition.vcf -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:testNoGTs--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcf4.1.example.vcf -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:testNonExistentSampleFile--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:testNonExistingSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:testNotFileVcfException--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/ -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:test that variant interval output filter mode is applied -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:testRemoveMLE--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample.withMLE.vcf -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:test removes variant line where '*' is only ALT allele --src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/spanning_deletion.vcf -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:test will not remove variant line where '*' is only ALT allele because --exclude-non-variants not called --src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/spanning_deletion.vcf -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:test encounter no instance of '*' as only ALT allele and ensure line is removed when only monomorphic allele existssrc/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/spanning_deletion.vcf -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:testRepeatedLineSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/test.dup.vcf -------------------------------------------------------------------------------- [15:55:21] Executing test SelectVariantsIntegrationTest:testSACDiploidsrc/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/diploid-multisample-sac.g.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testSACNonDiploidsrc/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/tetraploid-multisample-sac.g.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testSACSimpleDiploidsrc/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/261_S01_raw_variants_gvcf.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testSampleExclusionFromFileAndSeparateSample--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testSampleExclusionJustFromExpression--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testSampleExclusionJustFromFile--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testSampleExclusionJustFromRegexExpression--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testSampleInclusionWithNonexistingSamples--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testSampleSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:test select from multi allelic with exclude-non-variants --src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/multi-allelic.bi-allelicInGIH.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testSetFilteredGtoNocall--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/filteredSamples.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testSetFilteredGtoNocallUpdateInfo--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/selectVariantsInfoField.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testTetraDiploid--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/tetra-diploid.vcf -------------------------------------------------------------------------------- [15:55:22] Executing test SelectVariantsIntegrationTest:testTetraploid--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/tetraploid-multisample.vcf -------------------------------------------------------------------------------- [15:55:23] Executing test SelectVariantsIntegrationTest:testUnusedAlleleTrimming: (forHardLeftAlignVariantsTest.vcf,--remove-unused-alternates) -------------------------------------------------------------------------------- [15:55:23] Executing test SelectVariantsIntegrationTest:testUnusedAlleleTrimming: (forHardLeftAlignVariantsTest.vcf,(none)) -------------------------------------------------------------------------------- [15:55:23] Executing test SelectVariantsIntegrationTest:testUnusedAlleleTrimming: (multi-allelic-ordering.vcf,-sn SAMPLE-CC -sn SAMPLE-CT) -------------------------------------------------------------------------------- [15:55:23] Executing test SelectVariantsIntegrationTest:testUnusedAlleleTrimming: (multi-allelic-ordering.vcf,-sn SAMPLE-CC -sn SAMPLE-CT --exclude-non-variants) -------------------------------------------------------------------------------- [15:55:23] Executing test SelectVariantsIntegrationTest:testUnusedAlleleTrimming: (multi-allelic-ordering.vcf,-sn SAMPLE-CC -sn SAMPLE-CT --remove-unused-alternates) -------------------------------------------------------------------------------- [15:55:23] Executing test SelectVariantsIntegrationTest:testUnusedAlleleTrimming: (multi-allelic-ordering.vcf,-sn SAMPLE-CC -sn SAMPLE-CT --exclude-non-variants --remove-unused-alternates) -------------------------------------------------------------------------------- [15:55:23] Executing test SelectVariantsIntegrationTest:testVariantTypeSelection--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/complexExample1.vcf -------------------------------------------------------------------------------- [15:55:23] Executing test SelectVariantsIntegrationTest:testVariantTypeSelectionForGVCF--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/gvcfExample.g.vcf
Standard error
[May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848 [May 19, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1308622848