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

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

tests
0

failures
0

ignored
54.725s

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')) 0.377s 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')) 0.801s 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')) 6.727s 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')) 6.478s passed
testBQSRSpark[3](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 5.261s 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')) 7.032s 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')) 6.310s 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')) 6.518s 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')) 9.535s 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')) 2.773s 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')) 2.913s passed

Standard output

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[18:56:45] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
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[18:56:45] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
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[18:56:52] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
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[18:56:59] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark-
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[18:57:04] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --indels-context-size 4
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[18:57:11] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --low-quality-tail 5
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[18:57:17] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --quantizing-levels 6
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[18:57:24] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --mismatches-context-size 4
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[18:57:33] 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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[18:57:36] 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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[18:57:39] 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 19, 2025 at 6:56:45 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3378511872
[May 19, 2025 at 6:56:52 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3378511872
[May 19, 2025 at 6:56:59 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3378511872
[May 19, 2025 at 6:57:04 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=3378511872
[May 19, 2025 at 6:57:11 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.12 minutes.
Runtime.totalMemory()=3378511872
[May 19, 2025 at 6:57:17 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3378511872
[May 19, 2025 at 6:57:24 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3378511872
[May 19, 2025 at 6:57:33 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=3378511872
[May 19, 2025 at 6:57:36 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=3378511872
[May 19, 2025 at 6:57:39 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3378511872
[May 19, 2025 at 6:57:40 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3378511872