Class org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest

all > org.broadinstitute.hellbender.tools.spark > BaseRecalibratorSparkIntegrationTest
9

tests
0

failures
0

ignored
56.667s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.111s passed
testBQSRFailWithoutDBSNP 0.067s passed
testBQSRSparkCloud[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 4.812s 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')) 8.605s passed
testBQSRSparkCloud[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 6.963s 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')) 8.682s 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')) 8.244s 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')) 7.954s 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')) 11.229s passed

Standard output

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[22:44:18] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRFailWithIncompatibleReference
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[22:44:18] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRFailWithoutDBSNP
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[22:44:18] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq
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[22:44:23] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq
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[22:44:31] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud-
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[22:44:38] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --indels-context-size 4
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[22:44:47] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --low-quality-tail 5
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[22:44:55] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --quantizing-levels 6
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[22:45:03] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --mismatches-context-size 4

Standard error

[March 28, 2025 at 10:44:18 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
[March 28, 2025 at 10:44:23 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=849346560
[March 28, 2025 at 10:44:31 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=914358272
[March 28, 2025 at 10:44:38 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=914358272
[March 28, 2025 at 10:44:47 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=914358272
[March 28, 2025 at 10:44:55 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=914358272
[March 28, 2025 at 10:45:03 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=914358272
[March 28, 2025 at 10:45:14 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.19 minutes.
Runtime.totalMemory()=914358272