Class org.broadinstitute.hellbender.engine.CRAMSupportIntegrationTest

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

tests
0

failures
0

ignored
1m26.47s

duration
100%

successful

Tests

Test Duration Result
testNoRefMulti[0](cramtest.sam, cramtest.cram, .bam) 0.064s passed
testNoRef[0](cramtest.cram, .sam) 0.065s 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]) 0.119s 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]) 0.091s 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]) 0.117s 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]) 0.117s 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]) 0.066s 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]) 0.065s 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]) 0.116s 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]) 0.116s 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]) 0.115s 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]) 0.066s 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]) 0.072s 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]) 0.129s 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]) 0.091s 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]) 0.072s 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]) 0.073s 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]) 0.082s 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]) 0.077s 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]) 0.071s 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]) 0.071s 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]) 0.072s 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]) 0.083s 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]) 0.072s 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]) 0.127s 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]) 0.122s 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]) 0.119s 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]) 0.121s 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]) 0.118s 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]) 0.116s 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]) 0.124s 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]) 0.118s 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]) 0.116s 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]) 0.114s 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]) 0.114s 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]) 0.115s 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]) 0.076s 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]) 0.075s 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) 21.947s 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) 29.833s 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) 30.552s passed
testSamtoolsGeneratedCRAMSliceMD5Calculation 0.096s 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]) 0.167s 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]) 0.158s passed
testWrongRef[0](cramtest.cram, .sam, cramtestWrongRef.fasta) 0.063s passed

Standard error

[October 27, 2025 at 5:37:06 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:06 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:06 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:06 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:07 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:07 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:07 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:07 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:07 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:07 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:07 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:07 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:07 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:08 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:09 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:26 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.26 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:37:50 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.31 minutes.
Runtime.totalMemory()=1247805440
[October 27, 2025 at 5:38:20 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.31 minutes.
Runtime.totalMemory()=742391808
[October 27, 2025 at 5:38:32 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1981808640
[October 27, 2025 at 5:38:32 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1981808640
[October 27, 2025 at 5:38:32 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1981808640
[October 27, 2025 at 5:38:33 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1981808640