Class org.broadinstitute.hellbender.engine.CRAMSupportIntegrationTest

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

tests
0

failures
0

ignored
1m16.11s

duration
100%

successful

Tests

Test Duration Result
testNoRefMulti[0](cramtest.sam, cramtest.cram, .bam) 0.093s passed
testNoRef[0](cramtest.cram, .sam) 0.087s passed
testReadCramWithIntervalsWithBAIIndex[0](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000], [d, e]) 0.135s passed
testReadCramWithIntervalsWithBAIIndex[10](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000], [d, e]) 0.106s passed
testReadCramWithIntervalsWithBAIIndex[11](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-1099], [d]) 0.146s passed
testReadCramWithIntervalsWithBAIIndex[12](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1-200, 1:1000-2000], [a, d, e]) 0.145s passed
testReadCramWithIntervalsWithBAIIndex[13](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.097s passed
testReadCramWithIntervalsWithBAIIndex[14](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-399], [d, e, i]) 0.106s passed
testReadCramWithIntervalsWithBAIIndex[15](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000], [d, e]) 0.140s passed
testReadCramWithIntervalsWithBAIIndex[16](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-1099], [d]) 0.144s passed
testReadCramWithIntervalsWithBAIIndex[17](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1-200, 1:1000-2000], [a, d, e]) 0.142s passed
testReadCramWithIntervalsWithBAIIndex[18](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.096s passed
testReadCramWithIntervalsWithBAIIndex[19](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [1:1000-2000, 3:300-399], [d, e, i]) 0.095s passed
testReadCramWithIntervalsWithBAIIndex[1](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-1099], [d]) 0.162s passed
testReadCramWithIntervalsWithBAIIndex[20](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000], [d, e]) 0.120s passed
testReadCramWithIntervalsWithBAIIndex[21](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-1099], [d]) 0.102s passed
testReadCramWithIntervalsWithBAIIndex[22](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1-200, 1:1000-2000], [a, d, e]) 0.101s passed
testReadCramWithIntervalsWithBAIIndex[23](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.107s passed
testReadCramWithIntervalsWithBAIIndex[24](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-399], [d, e, i]) 0.103s passed
testReadCramWithIntervalsWithBAIIndex[25](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000], [d, e]) 0.120s passed
testReadCramWithIntervalsWithBAIIndex[26](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-1099], [d]) 0.102s passed
testReadCramWithIntervalsWithBAIIndex[27](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1-200, 1:1000-2000], [a, d, e]) 0.100s passed
testReadCramWithIntervalsWithBAIIndex[28](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.097s passed
testReadCramWithIntervalsWithBAIIndex[29](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [1:1000-2000, 3:300-399], [d, e, i]) 0.099s passed
testReadCramWithIntervalsWithBAIIndex[2](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1-200, 1:1000-2000], [a, d, e]) 0.171s passed
testReadCramWithIntervalsWithBAIIndex[3](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.160s passed
testReadCramWithIntervalsWithBAIIndex[4](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-399], [d, e, i]) 0.151s passed
testReadCramWithIntervalsWithBAIIndex[5](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000], [d, e]) 0.157s passed
testReadCramWithIntervalsWithBAIIndex[6](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-1099], [d]) 0.146s passed
testReadCramWithIntervalsWithBAIIndex[7](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1-200, 1:1000-2000], [a, d, e]) 0.139s passed
testReadCramWithIntervalsWithBAIIndex[8](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-400], [d, e, i, j]) 0.158s passed
testReadCramWithIntervalsWithBAIIndex[9](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [1:1000-2000, 3:300-399], [d, e, i]) 0.145s passed
testReadEntireCram[0](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [a, b, c, d, e, f, g, h, i, j, k]) 0.148s passed
testReadEntireCram[1](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .sam, [a, b, c, d, e, f, g, h, i, j, k]) 0.142s passed
testReadEntireCram[2](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [a, b, c, d, e, f, g, h, i, j, k]) 0.092s passed
testReadEntireCram[3](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .bam, [a, b, c, d, e, f, g, h, i, j, k]) 0.164s passed
testReadEntireCram[4](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_bai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [a, b, c, d, e, f, g, h, i, j, k]) 0.103s passed
testReadEntireCram[5](src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram, /gatkCloneMountPoint/src/test/resources/hg19mini.fasta, .cram, [a, b, c, d, e, f, g, h, i, j, k]) 0.103s passed
testRoundTripToCRAM[0](/gatkCloneMountPoint/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, true, false) 20.340s passed
testRoundTripToCRAM[1](/gatkCloneMountPoint/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, false, false) 25.770s passed
testRoundTripToCRAM[2](/gatkCloneMountPoint/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, false, false) 24.685s passed
testSamtoolsGeneratedCRAMSliceMD5Calculation 0.139s passed
testSerialQueriesOnRemoteFile[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/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]) 0.187s passed
testSerialQueriesOnRemoteFile[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/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]) 0.180s passed
testWrongRef[0](cramtest.cram, .sam, cramtestWrongRef.fasta) 0.086s passed

Standard error

[May 27, 2025 at 3:45:49 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:50 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:50 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:50 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:50 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:50 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:50 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:50 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:51 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:51 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:51 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:51 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:51 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:51 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:51 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:52 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:52 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:52 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:52 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:52 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:52 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:52 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:52 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:53 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:53 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:53 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:53 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:53 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:53 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:53 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:53 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:53 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:54 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:54 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:54 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:54 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:54 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:45:54 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:46:09 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.25 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 3:46:31 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.28 minutes.
Runtime.totalMemory()=979369984
[May 27, 2025 at 3:46:56 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.27 minutes.
Runtime.totalMemory()=1797259264
[May 27, 2025 at 3:47:05 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1797259264
[May 27, 2025 at 3:47:05 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1797259264
[May 27, 2025 at 3:47:05 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1797259264
[May 27, 2025 at 3:47:06 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1797259264