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

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

tests
0

failures
0

ignored
1m14.13s

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')) 0.422s 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')) 0.972s 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')) 9.002s 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')) 8.784s passed
testBQSRSpark[3](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 7.218s 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')) 9.766s 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')) 8.592s 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')) 8.552s 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')) 13.173s 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')) 3.730s 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')) 3.919s passed

Standard output

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[15:57:30] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
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[15:57:31] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
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[15:57:40] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
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[15:57:48] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark-
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[15:57:56] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --indels-context-size 4
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[15:58:05] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --low-quality-tail 5
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[15:58:14] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --quantizing-levels 6
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[15:58:23] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --mismatches-context-size 4
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[15:58:36] 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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[15:58:39] 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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[15:58:43] 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 3:57:31 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:57:40 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:57:48 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:57:56 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.12 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:58:05 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:58:14 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:58:23 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:58:36 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.22 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:58:39 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:58:43 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=3261071360
[May 27, 2025 at 3:58:44 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3261071360