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

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

tests
0

failures
0

ignored
5m31.30s

duration
100%

successful

Tests

Test Duration Result
testDifferentThreadValuesFromABucket[0](1) 5.272s passed
testDifferentThreadValuesFromABucket[1](2) 2.814s passed
testDifferentThreadValuesFromABucket[2](5) 2.350s 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 ) 3.703s 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 ) 3.471s 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 ) 3.129s 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 ) 3.195s 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 ) 2.716s 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 ) 2.696s 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 ) 2.426s 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 ) 2.479s passed
testGenomicsDBImportGCSInputs 3.178s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[0](1) 5.295s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[1](2) 4.337s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[2](3) 4.179s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[3](4) 4.155s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[4](100) 4.228s passed
testGenomicsDBImportGCSInputsInBatches[0](1) 2.616s passed
testGenomicsDBImportGCSInputsInBatches[1](2) 2.532s passed
testGenomicsDBImportGCSInputsInBatches[2](3) 2.576s passed
testGenomicsDBImportGCSInputsInBatches[3](4) 2.458s passed
testGenomicsDBImportGCSInputsInBatches[4](100) 2.511s passed
testUnindexedCloudGVCFsAreActuallyUnindexed 0.107s passed
testWriteToAndQueryFromGCS 2m11.29s passed
testWriteToAndQueryFromGCSUsingConnector 2m4.61s passed
testWriteToExistingGCSDirectory 2.975s passed

Standard error

[May 19, 2025 at 3:37:08 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.10431384499999968,Cpu time(s),0.08126034600000054
[May 19, 2025 at 3:37:11 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.07138167000000005,Cpu time(s),0.05845267899999969
[May 19, 2025 at 3:37:14 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.05350529499999994,Cpu time(s),0.042383162000000134
[May 19, 2025 at 3:37:17 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=838860800
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.022848219999999995,Cpu time(s),0.01897527900000003
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02639513399999989,Cpu time(s),0.022825795000000138
[May 19, 2025 at 3:37:21 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=838860800
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021735718999999973,Cpu time(s),0.01839949700000005
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.023269273999999958,Cpu time(s),0.020389209999999974
[May 19, 2025 at 3:37:24 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=838860800
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021518060000000016,Cpu time(s),0.01811200500000016
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02606592899999987,Cpu time(s),0.020403045999999897
[May 19, 2025 at 3:37:27 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=838860800
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02127731399999993,Cpu time(s),0.01818282100000006
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02290867699999998,Cpu time(s),0.020093879999999995
[May 19, 2025 at 3:37:30 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=838860800
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021140856999999878,Cpu time(s),0.01803148800000016
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02560231299999989,Cpu time(s),0.020311335999999992
[May 19, 2025 at 3:37:32 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=838860800
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.022073221999999934,Cpu time(s),0.018987876000000018
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.024193612999999937,Cpu time(s),0.021576462000000008
[May 19, 2025 at 3:37:35 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02118389799999998,Cpu time(s),0.017879481000000367
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.022686168999999975,Cpu time(s),0.01988550499999983
[May 19, 2025 at 3:37:37 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020876555000000036,Cpu time(s),0.017787680000000174
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02292017299999994,Cpu time(s),0.01996662199999987
[May 19, 2025 at 3:37:41 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020696975999999864,Cpu time(s),0.017632616000000146
[May 19, 2025 at 3:37:44 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02100395499999989,Cpu time(s),0.017827140000000175
[May 19, 2025 at 3:37:46 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021022548999999918,Cpu time(s),0.017840813000000302
[May 19, 2025 at 3:37:49 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021173769999999995,Cpu time(s),0.018028697000000236
[May 19, 2025 at 3:37:51 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021342576000000005,Cpu time(s),0.018024812000000234
[May 19, 2025 at 3:37:54 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02102178499999996,Cpu time(s),0.017966745000000162
[May 19, 2025 at 3:37:59 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020962043000000024,Cpu time(s),0.018014365000000178
[May 19, 2025 at 3:38:03 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020755173999999897,Cpu time(s),0.017760349000000238
[May 19, 2025 at 3:38:07 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020796015999999962,Cpu time(s),0.017783438000000255
[May 19, 2025 at 3:38:12 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020975975999999993,Cpu time(s),0.017858015000000144
[May 19, 2025 at 3:38:16 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020858910999999966,Cpu time(s),0.017783485000000293
[May 19, 2025 at 3:39:06 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.84 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020967708000000015,Cpu time(s),0.018046650000000244
[May 19, 2025 at 3:41:19 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.85 minutes.
Runtime.totalMemory()=853540864
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020842949999999947,Cpu time(s),0.017833217000000238
[May 19, 2025 at 3:42:35 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=853540864