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

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

tests
0

failures
0

ignored
5m30.10s

duration
100%

successful

Tests

Test Duration Result
testDifferentThreadValuesFromABucket[0](1) 4.406s passed
testDifferentThreadValuesFromABucket[1](2) 2.803s passed
testDifferentThreadValuesFromABucket[2](5) 1.991s 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 ) 2.472s 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 ) 2.631s 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 ) 2.400s 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 ) 2.636s 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 ) 2.140s 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 ) 2.483s 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 ) 2.246s 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 ) 2.571s passed
testGenomicsDBImportGCSInputs 2.472s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[0](1) 5.334s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[1](2) 4.178s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[2](3) 4.073s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[3](4) 4.074s passed
testGenomicsDBImportGCSInputsInBatchesNativeReader[4](100) 4.081s passed
testGenomicsDBImportGCSInputsInBatches[0](1) 2.651s passed
testGenomicsDBImportGCSInputsInBatches[1](2) 2.548s passed
testGenomicsDBImportGCSInputsInBatches[2](3) 2.430s passed
testGenomicsDBImportGCSInputsInBatches[3](4) 2.431s passed
testGenomicsDBImportGCSInputsInBatches[4](100) 2.481s passed
testUnindexedCloudGVCFsAreActuallyUnindexed 0.091s passed
testWriteToAndQueryFromGCS 2m8.98s passed
testWriteToAndQueryFromGCSUsingConnector 2m13.39s passed
testWriteToExistingGCSDirectory 2.110s passed

Standard error

[March 28, 2025 at 10:38:40 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.12949964500000005,Cpu time(s),0.1025986729999999
[March 28, 2025 at 10:38:44 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.06898996799999976,Cpu time(s),0.05507032199999989
[March 28, 2025 at 10:38:46 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.022810514000000053,Cpu time(s),0.01885572800000009
[March 28, 2025 at 10:38:48 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021009369999999958,Cpu time(s),0.018017014000000258
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.024431986000000114,Cpu time(s),0.0216036559999999
[March 28, 2025 at 10:38:51 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02176097099999992,Cpu time(s),0.01851840800000019
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.023292883000000004,Cpu time(s),0.02068811099999987
[March 28, 2025 at 10:38:53 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020845177999999836,Cpu time(s),0.018029355000000132
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.026207031999999963,Cpu time(s),0.020306823999999907
[March 28, 2025 at 10:38:56 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020705025999999967,Cpu time(s),0.017923520000000193
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.022964048999999962,Cpu time(s),0.020581204000000054
[March 28, 2025 at 10:38:58 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021267904999999955,Cpu time(s),0.018095359000000123
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.023064974000000044,Cpu time(s),0.02042838099999997
[March 28, 2025 at 10:39:00 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02233613400000003,Cpu time(s),0.01882625200000011
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02653762999999997,Cpu time(s),0.020570088999999948
[March 28, 2025 at 10:39:03 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021943344000000038,Cpu time(s),0.01859676700000007
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.023130176000000092,Cpu time(s),0.020518456999999896
[March 28, 2025 at 10:39:05 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021055325999999888,Cpu time(s),0.017892481000000234
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02398254899999994,Cpu time(s),0.020982636999999887
[March 28, 2025 at 10:39:08 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021344206000000008,Cpu time(s),0.01811973300000027
[March 28, 2025 at 10:39:11 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020928953000000017,Cpu time(s),0.017722792000000192
[March 28, 2025 at 10:39:13 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020964408000000007,Cpu time(s),0.017794942000000202
[March 28, 2025 at 10:39:16 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02100902499999993,Cpu time(s),0.017905267000000193
[March 28, 2025 at 10:39:18 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021309908000000016,Cpu time(s),0.01807384800000024
[March 28, 2025 at 10:39:21 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02122234299999995,Cpu time(s),0.018028622000000077
[March 28, 2025 at 10:39:26 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.022114237999999915,Cpu time(s),0.018714243000000144
[March 28, 2025 at 10:39:30 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.021002363999999975,Cpu time(s),0.017825822000000182
[March 28, 2025 at 10:39:34 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02107808199999998,Cpu time(s),0.017839235000000172
[March 28, 2025 at 10:39:38 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02087716199999993,Cpu time(s),0.017787272000000135
[March 28, 2025 at 10:39:42 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020275161999999933,Cpu time(s),0.017597038000000252
[March 28, 2025 at 10:40:36 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.88 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.02089690999999993,Cpu time(s),0.0178243970000002
[March 28, 2025 at 10:42:42 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.84 minutes.
Runtime.totalMemory()=849346560
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.020592782999999948,Cpu time(s),0.017620236000000133
[March 28, 2025 at 10:44:07 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=849346560