Class org.broadinstitute.hellbender.engine.CRAMSupportIntegrationTest

all > org.broadinstitute.hellbender.engine > CRAMSupportIntegrationTest
45

tests
0

failures
0

ignored
1m12.59s

duration
100%

successful

Tests

Test Duration Result
testNoRefMulti[0](cramtest.sam, cramtest.cram, .bam) 0.065s passed
testNoRef[0](cramtest.cram, .sam) 0.069s passed
testReadCramWithIntervalsWithBAIIndex[0](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000], [d, e]) 0.108s passed
testReadCramWithIntervalsWithBAIIndex[10](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000], [d, e]) 0.067s passed
testReadCramWithIntervalsWithBAIIndex[11](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [1:1000-1099], [d]) 0.142s passed
testReadCramWithIntervalsWithBAIIndex[12](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [1:1-200, 1:1000-2000], [a, d, e]) 0.121s passed
testReadCramWithIntervalsWithBAIIndex[13](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.067s passed
testReadCramWithIntervalsWithBAIIndex[14](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-399], [d, e, i]) 0.067s passed
testReadCramWithIntervalsWithBAIIndex[15](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000], [d, e]) 0.067s passed
testReadCramWithIntervalsWithBAIIndex[16](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [1:1000-1099], [d]) 0.119s passed
testReadCramWithIntervalsWithBAIIndex[17](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [1:1-200, 1:1000-2000], [a, d, e]) 0.117s passed
testReadCramWithIntervalsWithBAIIndex[18](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.071s passed
testReadCramWithIntervalsWithBAIIndex[19](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-399], [d, e, i]) 0.069s passed
testReadCramWithIntervalsWithBAIIndex[1](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [1:1000-1099], [d]) 0.127s passed
testReadCramWithIntervalsWithBAIIndex[20](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000], [d, e]) 0.099s passed
testReadCramWithIntervalsWithBAIIndex[21](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [1:1000-1099], [d]) 0.076s passed
testReadCramWithIntervalsWithBAIIndex[22](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [1:1-200, 1:1000-2000], [a, d, e]) 0.075s passed
testReadCramWithIntervalsWithBAIIndex[23](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.080s passed
testReadCramWithIntervalsWithBAIIndex[24](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-399], [d, e, i]) 0.078s passed
testReadCramWithIntervalsWithBAIIndex[25](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000], [d, e]) 0.073s passed
testReadCramWithIntervalsWithBAIIndex[26](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [1:1000-1099], [d]) 0.075s passed
testReadCramWithIntervalsWithBAIIndex[27](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [1:1-200, 1:1000-2000], [a, d, e]) 0.073s passed
testReadCramWithIntervalsWithBAIIndex[28](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.075s passed
testReadCramWithIntervalsWithBAIIndex[29](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-399], [d, e, i]) 0.081s passed
testReadCramWithIntervalsWithBAIIndex[2](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [1:1-200, 1:1000-2000], [a, d, e]) 0.140s passed
testReadCramWithIntervalsWithBAIIndex[3](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.130s passed
testReadCramWithIntervalsWithBAIIndex[4](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-399], [d, e, i]) 0.122s passed
testReadCramWithIntervalsWithBAIIndex[5](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000], [d, e]) 0.123s passed
testReadCramWithIntervalsWithBAIIndex[6](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [1:1000-1099], [d]) 0.122s passed
testReadCramWithIntervalsWithBAIIndex[7](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [1:1-200, 1:1000-2000], [a, d, e]) 0.117s passed
testReadCramWithIntervalsWithBAIIndex[8](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.127s passed
testReadCramWithIntervalsWithBAIIndex[9](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-399], [d, e, i]) 0.121s passed
testReadEntireCram[0](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [a, b, c, d, e, f, g, h, i, j, k]) 0.117s passed
testReadEntireCram[1](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .sam, [a, b, c, d, e, f, g, h, i, j, k]) 0.117s passed
testReadEntireCram[2](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [a, b, c, d, e, f, g, h, i, j, k]) 0.115s passed
testReadEntireCram[3](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .bam, [a, b, c, d, e, f, g, h, i, j, k]) 0.119s passed
testReadEntireCram[4](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [a, b, c, d, e, f, g, h, i, j, k]) 0.078s passed
testReadEntireCram[5](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, .cram, [a, b, c, d, e, f, g, h, i, j, k]) 0.087s passed
testRoundTripToCRAM[0](/home/runner/work/gatk/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, true, false) 19.419s passed
testRoundTripToCRAM[1](/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, false, false) 24.738s passed
testRoundTripToCRAM[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, false, false) 24.252s passed
testSamtoolsGeneratedCRAMSliceMD5Calculation 0.085s passed
testSerialQueriesOnRemoteFile[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000009-10000011, unmapped], [a, b, c, d, e, g, h, h, i, i], [g, h, h, i, i]) 0.174s passed
testSerialQueriesOnRemoteFile[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000009-10000013, unmapped], [a, b, c, d, e, f, f, g, h, h, i, i], [g, h, h, i, i]) 0.159s passed
testWrongRef[0](cramtest.cram, .sam, cramtestWrongRef.fasta) 0.064s passed

Standard error

[May 27, 2025 at 2:44:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:12 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:12 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:44:26 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.24 minutes.
Runtime.totalMemory()=750780416
[May 27, 2025 at 2:44:47 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.26 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 2:45:11 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.26 minutes.
Runtime.totalMemory()=1623195648
[May 27, 2025 at 2:45:20 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1965031424
[May 27, 2025 at 2:45:20 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1965031424
[May 27, 2025 at 2:45:20 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1965031424
[May 27, 2025 at 2:45:21 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1965031424