Class org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSparkIntegrationTest

all > org.broadinstitute.hellbender.tools.copynumber > CollectAllelicCountsSparkIntegrationTest
4

tests
0

failures
0

ignored
2.593s

duration
100%

successful

Tests

Test Duration Result
test[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/collect-allelic-counts-normal.bam, AbstractRecordCollection{metadata=SimpleSampleLocatableMetadata{sampleMetadata=SimpleSampleMetadata{sampleName='20'}, locatableMetadata=SimpleLocatableMetadata{sequenceDictionary=SAMSequenceDictionary:( sequences:4 length:64000 md5:5508371427589f82040a586d73c0aa6f)}}, records=[AllelicCount{interval=1:10736-10736, refReadCount=0, altReadCount=0, refNucleotide=G, altNucleotide=N}, AllelicCount{interval=1:11522-11522, refReadCount=7, altReadCount=4, refNucleotide=G, altNucleotide=A}, AllelicCount{interval=1:12098-12098, refReadCount=8, altReadCount=6, refNucleotide=G, altNucleotide=T}, AllelicCount{interval=1:12444-12444, refReadCount=0, altReadCount=18, refNucleotide=T, altNucleotide=C}, AllelicCount{interval=1:13059-13059, refReadCount=0, altReadCount=8, refNucleotide=C, altNucleotide=A}, AllelicCount{interval=1:14630-14630, refReadCount=9, altReadCount=8, refNucleotide=T, altNucleotide=G}, AllelicCount{interval=1:15204-15204, refReadCount=4, altReadCount=4, refNucleotide=C, altNucleotide=A}, AllelicCount{interval=2:14689-14689, refReadCount=6, altReadCount=9, refNucleotide=T, altNucleotide=G}, AllelicCount{interval=2:14982-14982, refReadCount=6, altReadCount=5, refNucleotide=G, altNucleotide=C}, AllelicCount{interval=2:15110-15110, refReadCount=6, altReadCount=0, refNucleotide=G, altNucleotide=N}, AllelicCount{interval=2:15629-15629, refReadCount=5, altReadCount=3, refNucleotide=T, altNucleotide=A}]}) 0.904s passed
test[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/collect-allelic-counts-tumor.bam, AbstractRecordCollection{metadata=SimpleSampleLocatableMetadata{sampleMetadata=SimpleSampleMetadata{sampleName='20'}, locatableMetadata=SimpleLocatableMetadata{sequenceDictionary=SAMSequenceDictionary:( sequences:4 length:64000 md5:5508371427589f82040a586d73c0aa6f)}}, records=[AllelicCount{interval=1:10736-10736, refReadCount=0, altReadCount=0, refNucleotide=G, altNucleotide=N}, AllelicCount{interval=1:11522-11522, refReadCount=7, altReadCount=4, refNucleotide=G, altNucleotide=A}, AllelicCount{interval=1:12098-12098, refReadCount=8, altReadCount=6, refNucleotide=G, altNucleotide=T}, AllelicCount{interval=1:12444-12444, refReadCount=0, altReadCount=17, refNucleotide=T, altNucleotide=C}, AllelicCount{interval=1:13059-13059, refReadCount=0, altReadCount=8, refNucleotide=C, altNucleotide=A}, AllelicCount{interval=1:14630-14630, refReadCount=9, altReadCount=8, refNucleotide=T, altNucleotide=G}, AllelicCount{interval=1:15204-15204, refReadCount=4, altReadCount=3, refNucleotide=C, altNucleotide=A}, AllelicCount{interval=2:14689-14689, refReadCount=6, altReadCount=9, refNucleotide=T, altNucleotide=G}, AllelicCount{interval=2:14982-14982, refReadCount=6, altReadCount=5, refNucleotide=G, altNucleotide=C}, AllelicCount{interval=2:15110-15110, refReadCount=6, altReadCount=0, refNucleotide=G, altNucleotide=N}, AllelicCount{interval=2:15629-15629, refReadCount=5, altReadCount=3, refNucleotide=T, altNucleotide=A}]}) 0.530s passed
test[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/collect-allelic-counts-normal.bam, AbstractRecordCollection{metadata=SimpleSampleLocatableMetadata{sampleMetadata=SimpleSampleMetadata{sampleName='20'}, locatableMetadata=SimpleLocatableMetadata{sequenceDictionary=SAMSequenceDictionary:( sequences:4 length:64000 md5:5508371427589f82040a586d73c0aa6f)}}, records=[AllelicCount{interval=1:10736-10736, refReadCount=0, altReadCount=0, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:11522-11522, refReadCount=7, altReadCount=4, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:12098-12098, refReadCount=8, altReadCount=6, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:12444-12444, refReadCount=0, altReadCount=18, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:13059-13059, refReadCount=0, altReadCount=8, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:14630-14630, refReadCount=9, altReadCount=8, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:15204-15204, refReadCount=4, altReadCount=4, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=2:14689-14689, refReadCount=6, altReadCount=9, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=2:14982-14982, refReadCount=6, altReadCount=5, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=2:15110-15110, refReadCount=6, altReadCount=0, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=2:15629-15629, refReadCount=5, altReadCount=3, refNucleotide=N, altNucleotide=N}]}) 0.633s passed
test[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/collect-allelic-counts-tumor.bam, AbstractRecordCollection{metadata=SimpleSampleLocatableMetadata{sampleMetadata=SimpleSampleMetadata{sampleName='20'}, locatableMetadata=SimpleLocatableMetadata{sequenceDictionary=SAMSequenceDictionary:( sequences:4 length:64000 md5:5508371427589f82040a586d73c0aa6f)}}, records=[AllelicCount{interval=1:10736-10736, refReadCount=0, altReadCount=0, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:11522-11522, refReadCount=7, altReadCount=4, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:12098-12098, refReadCount=8, altReadCount=6, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:12444-12444, refReadCount=0, altReadCount=17, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:13059-13059, refReadCount=0, altReadCount=8, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:14630-14630, refReadCount=9, altReadCount=8, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=1:15204-15204, refReadCount=4, altReadCount=3, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=2:14689-14689, refReadCount=6, altReadCount=9, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=2:14982-14982, refReadCount=6, altReadCount=5, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=2:15110-15110, refReadCount=6, altReadCount=0, refNucleotide=N, altNucleotide=N}, AllelicCount{interval=2:15629-15629, refReadCount=5, altReadCount=3, refNucleotide=N, altNucleotide=N}]}) 0.526s passed

Standard error

[March 28, 2025 at 10:35:52 PM UTC] org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:35:53 PM UTC] org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:35:53 PM UTC] org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:35:54 PM UTC] org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000