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

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

tests
0

failures
0

ignored
48.070s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.105s passed
testBQSRFailWithoutDBSNP 0.059s passed
testBQSRSparkCloud[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 5.944s 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')) 6.798s passed
testBQSRSparkCloud[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 6.150s 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')) 6.962s 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')) 6.470s 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')) 6.297s 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')) 9.285s passed

Standard output

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[17:45:11] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRFailWithIncompatibleReference
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[17:45:11] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRFailWithoutDBSNP
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[17:45:11] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq
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[17:45:17] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq
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[17:45:24] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud-
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[17:45:30] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --indels-context-size 4
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[17:45:37] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --low-quality-tail 5
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[17:45:43] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --quantizing-levels 6
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[17:45:49] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --mismatches-context-size 4

Standard error

[October 27, 2025 at 5:45:11 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=874512384
[October 27, 2025 at 5:45:17 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=874512384
[October 27, 2025 at 5:45:24 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=874512384
[October 27, 2025 at 5:45:30 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=1839202304
[October 27, 2025 at 5:45:37 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1839202304
[October 27, 2025 at 5:45:43 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1006632960
[October 27, 2025 at 5:45:49 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=1006632960
[October 27, 2025 at 5:45:59 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1006632960