Class org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest
Tests
| Test |
Duration |
Result |
| testBQSRFailWithIncompatibleReference |
0.115s |
passed |
| testBQSRFailWithoutDBSNP |
0.071s |
passed |
| testBQSRSparkCloud[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) |
4.934s |
passed |
| testBQSRSparkCloud[1](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq')) |
8.565s |
passed |
| testBQSRSparkCloud[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) |
7.150s |
passed |
| testBQSRSparkCloud[3](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --indels-context-size 4')) |
9.325s |
passed |
| testBQSRSparkCloud[4](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --low-quality-tail 5')) |
8.106s |
passed |
| testBQSRSparkCloud[5](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --quantizing-levels 6')) |
8.019s |
passed |
| testBQSRSparkCloud[6](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --mismatches-context-size 4')) |
11.521s |
passed |
Standard output
--------------------------------------------------------------------------------
[15:42:47] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRFailWithIncompatibleReference
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[15:42:47] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRFailWithoutDBSNP
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[15:42:47] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq
--------------------------------------------------------------------------------
[15:42:52] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq
--------------------------------------------------------------------------------
[15:43:00] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud-
--------------------------------------------------------------------------------
[15:43:08] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --indels-context-size 4
--------------------------------------------------------------------------------
[15:43:17] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --low-quality-tail 5
--------------------------------------------------------------------------------
[15:43:25] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --quantizing-levels 6
--------------------------------------------------------------------------------
[15:43:33] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --mismatches-context-size 4
Standard error
[May 19, 2025 at 3:42:47 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=838860800
[May 19, 2025 at 3:42:52 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=838860800
[May 19, 2025 at 3:43:00 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1042284544
[May 19, 2025 at 3:43:08 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.12 minutes.
Runtime.totalMemory()=1042284544
[May 19, 2025 at 3:43:17 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=954204160
[May 19, 2025 at 3:43:25 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=954204160
[May 19, 2025 at 3:43:33 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=943718400
[May 19, 2025 at 3:43:45 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.19 minutes.
Runtime.totalMemory()=943718400