Class org.broadinstitute.hellbender.tools.CRAMIssue8768DetectorIntegrationTest

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

tests
0

failures
0

ignored
1m51.99s

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) 0.438s 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) 0.247s 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) 0.960s 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) 4.827s 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) 0.300s 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) 0.323s 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) 1m44.89s 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

[March 28, 2025 at 10:32:27 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:32:27 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:32:28 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:32:33 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=775946240
[March 28, 2025 at 10:32:33 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=775946240
[March 28, 2025 at 10:32:33 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=775946240
[March 28, 2025 at 10:34:18 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 1.75 minutes.
Runtime.totalMemory()=803209216