Class org.broadinstitute.hellbender.engine.CRAMSupportIntegrationTest

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

tests
0

failures
0

ignored
1m19.78s

duration
100%

successful

Tests

Test Duration Result
testNoRefMulti[0](cramtest.sam, cramtest.cram, .bam) 0.073s passed
testNoRef[0](cramtest.cram, .sam) 0.073s 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]) 0.137s 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]) 0.072s 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]) 0.134s 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]) 0.073s 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]) 0.073s 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]) 0.078s 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]) 0.134s 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]) 0.124s 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]) 0.124s 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]) 0.074s 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]) 0.084s 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]) 0.134s 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]) 0.102s 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]) 0.082s 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]) 0.082s 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]) 0.089s 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]) 0.084s 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]) 0.078s 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]) 0.077s 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]) 0.077s 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]) 0.091s 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]) 0.152s 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]) 0.147s 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]) 0.129s 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]) 0.128s 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]) 0.126s 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]) 0.123s 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]) 0.128s 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]) 0.123s 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]) 0.124s 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]) 0.123s 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]) 0.124s 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]) 0.123s 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]) 0.079s 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]) 0.080s 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) 21.087s 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) 27.769s 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) 26.493s passed
testSamtoolsGeneratedCRAMSliceMD5Calculation 0.089s 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]) 0.161s passed
testWrongRef[0](cramtest.cram, .sam, cramtestWrongRef.fasta) 0.070s passed

Standard error

[June 2, 2025 at 2:07:37 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:37 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:37 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:37 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:37 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:37 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:38 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:38 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:38 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:38 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:38 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:38 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:38 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:38 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:38 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:39 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:39 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:39 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:39 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:39 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:39 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:39 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:39 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:39 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:39 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:40 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:40 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:40 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:40 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:40 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:40 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:40 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:40 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:40 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:40 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:41 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:41 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:41 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:07:56 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.26 minutes.
Runtime.totalMemory()=629145600
[June 2, 2025 at 2:08:20 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=889192448
[June 2, 2025 at 2:08:47 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.29 minutes.
Runtime.totalMemory()=1539309568
[June 2, 2025 at 2:08:56 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1845493760
[June 2, 2025 at 2:08:56 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1845493760
[June 2, 2025 at 2:08:56 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1845493760
[June 2, 2025 at 2:08:57 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1845493760