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

all > org.broadinstitute.hellbender.tools.spark > BaseRecalibratorSparkIntegrationTest
11

tests
0

failures
0

ignored
1m16.29s

duration
100%

successful

Tests

Test Duration Result
testBQSRSpark[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.471s passed
testBQSRSpark[10](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf')) 1.007s passed
testBQSRSpark[1](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq')) 9.542s passed
testBQSRSpark[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq')) 9.174s passed
testBQSRSpark[3](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 7.336s passed
testBQSRSpark[4](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')) 10.079s passed
testBQSRSpark[5](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')) 8.754s passed
testBQSRSpark[6](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')) 8.725s passed
testBQSRSpark[7](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')) 13.391s passed
testBQSRSpark[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.bam', args='-indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf')) 3.825s passed
testBQSRSpark[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram', args='-indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf')) 3.984s passed

Standard output

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[18:28:31] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
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[18:28:32] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
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[18:28:41] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
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[18:28:50] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark-
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[18:28:58] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --indels-context-size 4
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[18:29:08] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --low-quality-tail 5
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[18:29:17] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --quantizing-levels 6
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[18:29:25] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --mismatches-context-size 4
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[18:29:39] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf
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[18:29:42] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf
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[18:29:46] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf

Standard error

[May 27, 2025 at 6:28:32 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3166699520
[May 27, 2025 at 6:28:41 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=3166699520
[May 27, 2025 at 6:28:50 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=3166699520
[May 27, 2025 at 6:28:58 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.12 minutes.
Runtime.totalMemory()=3166699520
[May 27, 2025 at 6:29:08 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.17 minutes.
Runtime.totalMemory()=3166699520
[May 27, 2025 at 6:29:17 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=3166699520
[May 27, 2025 at 6:29:25 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=3166699520
[May 27, 2025 at 6:29:39 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.22 minutes.
Runtime.totalMemory()=3166699520
[May 27, 2025 at 6:29:42 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=3166699520
[May 27, 2025 at 6:29:46 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=3166699520
[May 27, 2025 at 6:29:47 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3166699520