Class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest

all > org.broadinstitute.hellbender.tools.genomicsdb > GenomicsDBImportIntegrationTest
26

tests
0

failures
0

ignored
3m28.54s

duration
100%

successful

Tests

Test Duration Result
testDifferentThreadValuesFromABucket[0](1) 4.281s passed
testDifferentThreadValuesFromABucket[1](2) 2.424s passed
testDifferentThreadValuesFromABucket[2](5) 2.004s passed
testExplicitIndicesInSampleNameMapInTheCloud[0](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.gz.tbi HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.gz.tbi ) 2.629s passed
testExplicitIndicesInSampleNameMapInTheCloud[1](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.idx HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.idx ) 2.802s passed
testExplicitIndicesInSampleNameMapInTheCloud[2](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf.gz HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf.gz ) 2.585s passed
testExplicitIndicesInSampleNameMapInTheCloud[3](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf ) 2.572s passed
testExplicitIndicesInSampleNameMapInTheCloud[4](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.gz.tbi HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.gz.tbi ) 1.944s passed
testExplicitIndicesInSampleNameMapInTheCloud[5](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.idx HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.idx ) 2.413s passed
testExplicitIndicesInSampleNameMapInTheCloud[6](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf.gz HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf.gz ) 1.860s passed
testExplicitIndicesInSampleNameMapInTheCloud[7](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf ) 2.755s passed
testGenomicsDBImportGCSInputs 2.228s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[0](1) 4.443s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[1](2) 3.657s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[2](3) 3.488s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[3](4) 3.445s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[4](100) 3.765s passed
testGenomicsDBImportGCSInputsInBatches[0](1) 2.260s passed
testGenomicsDBImportGCSInputsInBatches[1](2) 2.172s passed
testGenomicsDBImportGCSInputsInBatches[2](3) 3.020s passed
testGenomicsDBImportGCSInputsInBatches[3](4) 2.374s passed
testGenomicsDBImportGCSInputsInBatches[4](100) 2.151s passed
testUnindexedCloudGVCFsAreActuallyUnindexed 0.076s passed
testWriteToAndQueryFromGCS 1m13.97s passed
testWriteToAndQueryFromGCSUsingConnector 1m11.94s passed
testWriteToExistingGCSDirectory 1.283s passed

Standard error

[June 12, 2025 at 8:45:28 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=884998144
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.099398091,Cpu time(s),0.0789345180000003
[June 12, 2025 at 8:45:31 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=884998144
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.0719231239999998,Cpu time(s),0.057127700000000003
[June 12, 2025 at 8:45:33 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=884998144
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.053702444999999974,Cpu time(s),0.04583672599999981
[June 12, 2025 at 8:45:36 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=868220928
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020525821999999905,Cpu time(s),0.017979093000000158
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02506412999999988,Cpu time(s),0.022462675999999928
[June 12, 2025 at 8:45:38 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=868220928
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021167465999999954,Cpu time(s),0.01828733999999998
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02419499800000005,Cpu time(s),0.021668215999999976
[June 12, 2025 at 8:45:41 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=868220928
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020754434999999908,Cpu time(s),0.01823511199999997
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.023493439999999814,Cpu time(s),0.020878069999999936
[June 12, 2025 at 8:45:44 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=868220928
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.022408555999999833,Cpu time(s),0.019212547999999954
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02313758500000004,Cpu time(s),0.020765756999999985
[June 12, 2025 at 8:45:46 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=880803840
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021022831999999873,Cpu time(s),0.01812104899999995
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.023193138000000023,Cpu time(s),0.02066495999999998
[June 12, 2025 at 8:45:48 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=880803840
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02097679100000004,Cpu time(s),0.018067444999999988
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.025692654999999898,Cpu time(s),0.020618928999999956
[June 12, 2025 at 8:45:50 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=880803840
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021211458000000016,Cpu time(s),0.01816373300000013
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.023826331000000006,Cpu time(s),0.021062458999999926
[June 12, 2025 at 8:45:53 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=880803840
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020769057999999938,Cpu time(s),0.01819022599999997
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.023572584999999886,Cpu time(s),0.021012506999999958
[June 12, 2025 at 8:45:55 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020958728999999916,Cpu time(s),0.018173929999999977
[June 12, 2025 at 8:45:57 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021122998000000004,Cpu time(s),0.018369532999999827
[June 12, 2025 at 8:46:00 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020869277999999953,Cpu time(s),0.018114400000000093
[June 12, 2025 at 8:46:03 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020776899999999987,Cpu time(s),0.018156260000000042
[June 12, 2025 at 8:46:05 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021393357000000057,Cpu time(s),0.018364612999999967
[June 12, 2025 at 8:46:07 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.0209235119999999,Cpu time(s),0.018012338000000145
[June 12, 2025 at 8:46:12 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02097976300000005,Cpu time(s),0.018145838999999976
[June 12, 2025 at 8:46:15 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020943061999999988,Cpu time(s),0.01802170300000017
[June 12, 2025 at 8:46:19 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020667161999999958,Cpu time(s),0.017929841000000092
[June 12, 2025 at 8:46:22 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02046694999999989,Cpu time(s),0.017820942000000138
[June 12, 2025 at 8:46:26 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020687886999999922,Cpu time(s),0.01816891600000003
[June 12, 2025 at 8:47:00 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.56 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02052287500000001,Cpu time(s),0.017824161000000113
[June 12, 2025 at 8:48:13 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.55 minutes.
Runtime.totalMemory()=874512384
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02062394499999989,Cpu time(s),0.018146501999999988
[June 12, 2025 at 8:48:53 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=874512384