Class org.broadinstitute.hellbender.tools.CRAMIssue8768DetectorIntegrationTest

all > org.broadinstitute.hellbender.tools > CRAMIssue8768DetectorIntegrationTest

tests

failures

ignored

2m0.32s

duration

100%

successful

Tests
Standard output
Standard error

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)	0.397s	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)	0.227s	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)	0.840s	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)	4.513s	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)	0.293s	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)	0.340s	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)	1m53.71s	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

[May 19, 2025 at 3:31:05 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=541065216
[May 19, 2025 at 3:31:05 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=541065216
[May 19, 2025 at 3:31:06 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=606076928
[May 19, 2025 at 3:31:10 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=595591168
[May 19, 2025 at 3:31:11 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=595591168
[May 19, 2025 at 3:31:11 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=595591168
[May 19, 2025 at 3:33:05 PM UTC] org.broadinstitute.hellbender.tools.CRAMIssue8768Detector done. Elapsed time: 1.89 minutes.
Runtime.totalMemory()=595591168