Class org.broadinstitute.hellbender.tools.CRAMIssue8768DetectorIntegrationTest

all > org.broadinstitute.hellbender.tools > CRAMIssue8768DetectorIntegrationTest
7

tests
0

failures
0

ignored
3m16.53s

duration
100%

successful

Tests

Test Duration Result
testCramAnalysis[0](src/test/resources/filediagnostics/thisFileIsCorruptMito.bug8768.cram, src/test/resources/filediagnostics/mitoCorrupt.bug8768.fa, [(verbose,false)], src/test/resources/filediagnostics/thisFileIsCorruptMito.false.bug8768.txt, src/test/resources/filediagnostics/thisFileIsCorruptMito.false.bug8768.tsv) 0.408s passed
testCramAnalysis[1](src/test/resources/filediagnostics/thisFileIsCorruptMito.bug8768.cram, src/test/resources/filediagnostics/mitoCorrupt.bug8768.fa, [(verbose,true)], src/test/resources/filediagnostics/thisFileIsCorruptMito.true.bug8768.txt, src/test/resources/filediagnostics/thisFileIsCorruptMito.true.bug8768.tsv) 0.245s passed
testCramAnalysis[2](/home/runner/work/gatk/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [(verbose,false)], src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.txt, src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.tsv) 0.980s passed
testCramAnalysis[3](/home/runner/work/gatk/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [(verbose,true)], src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.txt, src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.tsv) 6.457s passed
testCramAnalysis[4](src/test/resources/filediagnostics/thisFileIsCorruptMito.2BadContainers.bug8768.cram, src/test/resources/filediagnostics/mitoCorrupt.bug8768.fa, [(verbose,false)], src/test/resources/filediagnostics/thisFileIsCorruptMito.2BadContainers.false.bug8768.txt, src/test/resources/filediagnostics/thisFileIsCorruptMito.2BadContainers.false.bug8768.tsv) 0.340s passed
testCramAnalysis[5](src/test/resources/filediagnostics/thisFileIsCorruptMito.3BadContainers.bug8768.cram, src/test/resources/filediagnostics/mitoCorrupt.bug8768.fa, [(verbose,false)], src/test/resources/filediagnostics/thisFileIsCorruptMito.3BadContainers.false.bug8768.txt, src/test/resources/filediagnostics/thisFileIsCorruptMito.3BadContainers.false.bug8768.tsv) 0.384s passed
testCramAnalysis[6](gs://hellbender/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram, gs://hellbender/test/resources/large/human_g1k_v37.20.21.fasta, [(verbose,false)], src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.cloud.txt, src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.cloud.tsv) 3m7.71s passed

Standard output

**********************!!!!!Possible CORRUPT CONTAINERS DETECTED!!!!!**********************:


**********************!!!!!Possible CORRUPT CONTAINERS DETECTED!!!!!**********************:


**********************NO CORRUPT CONTAINERS DETECTED**********************

**********************NO CORRUPT CONTAINERS DETECTED**********************

**********************!!!!!Possible CORRUPT CONTAINERS DETECTED!!!!!**********************:


**********************!!!!!Possible CORRUPT CONTAINERS DETECTED!!!!!**********************:


**********************NO CORRUPT CONTAINERS DETECTED**********************

Standard error

[October 27, 2025 at 5:37:37 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=534773760
[October 27, 2025 at 5:37:37 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=534773760
[October 27, 2025 at 5:37:38 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=534773760
[October 27, 2025 at 5:37:45 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1409286144
[October 27, 2025 at 5:37:45 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1409286144
[October 27, 2025 at 5:37:45 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1409286144
[October 27, 2025 at 5:40:53 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 3.13 minutes.
Runtime.totalMemory()=1279262720