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

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

tests
0

failures
0

ignored
53.946s

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')) 0.396s 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')) 0.802s 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')) 6.646s 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')) 6.341s passed
testBQSRSpark[3](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 5.182s 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')) 6.910s 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')) 6.418s 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')) 6.100s 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')) 9.489s 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')) 2.758s 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')) 2.904s passed

Standard output

--------------------------------------------------------------------------------
[13:46:56] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
--------------------------------------------------------------------------------
[13:46:56] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
--------------------------------------------------------------------------------
[13:47:03] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
--------------------------------------------------------------------------------
[13:47:09] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark-
--------------------------------------------------------------------------------
[13:47:15] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --indels-context-size 4
--------------------------------------------------------------------------------
[13:47:21] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --low-quality-tail 5
--------------------------------------------------------------------------------
[13:47:28] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --quantizing-levels 6
--------------------------------------------------------------------------------
[13:47:34] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --mismatches-context-size 4
--------------------------------------------------------------------------------
[13:47:44] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf
--------------------------------------------------------------------------------
[13:47:46] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf
--------------------------------------------------------------------------------
[13:47:49] 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 1:46:56 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3177185280
[May 27, 2025 at 1:47:03 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3177185280
[May 27, 2025 at 1:47:09 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3177185280
[May 27, 2025 at 1:47:15 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=3177185280
[May 27, 2025 at 1:47:21 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3177185280
[May 27, 2025 at 1:47:28 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=3177185280
[May 27, 2025 at 1:47:34 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=3177185280
[May 27, 2025 at 1:47:43 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=3177185280
[May 27, 2025 at 1:47:46 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=3177185280
[May 27, 2025 at 1:47:49 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=3177185280
[May 27, 2025 at 1:47:50 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=3177185280