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

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

tests
0

failures
0

ignored
53.832s

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')) 0.366s 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')) 0.778s 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')) 6.694s 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')) 6.380s passed
testBQSRSpark[3](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 5.172s 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')) 6.897s 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')) 6.206s 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')) 6.129s 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')) 9.469s 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')) 2.808s 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')) 2.933s passed

Standard output

--------------------------------------------------------------------------------
[18:12:37] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
--------------------------------------------------------------------------------
[18:12:37] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
--------------------------------------------------------------------------------
[18:12:44] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
--------------------------------------------------------------------------------
[18:12:50] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark-
--------------------------------------------------------------------------------
[18:12:56] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --indels-context-size 4
--------------------------------------------------------------------------------
[18:13:02] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --low-quality-tail 5
--------------------------------------------------------------------------------
[18:13:09] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --quantizing-levels 6
--------------------------------------------------------------------------------
[18:13:15] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --mismatches-context-size 4
--------------------------------------------------------------------------------
[18:13:24] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf
--------------------------------------------------------------------------------
[18:13:27] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf
--------------------------------------------------------------------------------
[18:13:30] 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 6:12:37 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3045064704
[May 27, 2025 at 6:12:44 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3045064704
[May 27, 2025 at 6:12:50 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3045064704
[May 27, 2025 at 6:12:56 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=3045064704
[May 27, 2025 at 6:13:02 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3045064704
[May 27, 2025 at 6:13:09 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3045064704
[May 27, 2025 at 6:13:15 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3045064704
[May 27, 2025 at 6:13:24 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=3084910592
[May 27, 2025 at 6:13:27 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3084910592
[May 27, 2025 at 6:13:30 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2462056448
[May 27, 2025 at 6:13:31 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2462056448