Class org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSparkIntegrationTest

all > org.broadinstitute.hellbender.tools.spark.pipelines > BQSRPipelineSparkIntegrationTest
3

tests
0

failures
0

ignored
5.527s

duration
100%

successful

Tests

Test Duration Result
testBQSRLocalRef[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --use-original-qualities false')) 2.480s passed
testBQSRLocalRef[1](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')) 1.101s passed
testBQSRLocalRef[2](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')) 1.946s passed

Standard error

[October 27, 2025 at 5:46:56 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=935329792
[Mon Oct 27 17:46:56 UTC 2025] SortSam --INPUT /tmp/local16469784102307886954/bqsrSparkPipelineTest5857759767171335840.bam --OUTPUT /tmp/local16469784102307886954/resultsFileSorted13128161723796470104.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Oct 27 17:46:56 UTC 2025] Executing as runner@runnervmrcw8b on Linux 6.11.0-1018-azure aarch64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: Version:3.4.0
INFO	2025-10-27 17:46:56	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Oct 27 17:46:56 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=935329792
[Mon Oct 27 17:46:56 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recalibrated.DIQ.bam --OUTPUT /tmp/local16469784102307886954/expectedFileSorted9951992438602779099.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Oct 27 17:46:56 UTC 2025] Executing as runner@runnervmrcw8b on Linux 6.11.0-1018-azure aarch64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: Version:3.4.0
INFO	2025-10-27 17:46:56	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Oct 27 17:46:56 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=935329792
[October 27, 2025 at 5:46:57 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=935329792
[Mon Oct 27 17:46:57 UTC 2025] SortSam --INPUT /tmp/local16469784102307886954/bqsrSparkPipelineTest16570712882169815395.bam --OUTPUT /tmp/local16469784102307886954/resultsFileSorted18106347126274669381.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Oct 27 17:46:57 UTC 2025] Executing as runner@runnervmrcw8b on Linux 6.11.0-1018-azure aarch64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: Version:3.4.0
INFO	2025-10-27 17:46:57	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Oct 27 17:46:57 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=935329792
[Mon Oct 27 17:46:57 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.bam --OUTPUT /tmp/local16469784102307886954/expectedFileSorted1034149258354638789.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Oct 27 17:46:57 UTC 2025] Executing as runner@runnervmrcw8b on Linux 6.11.0-1018-azure aarch64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: Version:3.4.0
INFO	2025-10-27 17:46:57	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Oct 27 17:46:57 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=935329792
[October 27, 2025 at 5:46:59 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1604321280
[Mon Oct 27 17:46:59 UTC 2025] SortSam --INPUT /tmp/local16469784102307886954/bqsrSparkPipelineTest8731045550214594760.cram --OUTPUT /tmp/local16469784102307886954/resultsFileSorted6413560362995568372.cram --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Oct 27 17:46:59 UTC 2025] Executing as runner@runnervmrcw8b on Linux 6.11.0-1018-azure aarch64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: Version:3.4.0
INFO	2025-10-27 17:46:59	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Oct 27 17:46:59 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1604321280
[Mon Oct 27 17:46:59 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.cram --OUTPUT /tmp/local16469784102307886954/expectedFileSorted18044958563344155977.cram --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Oct 27 17:46:59 UTC 2025] Executing as runner@runnervmrcw8b on Linux 6.11.0-1018-azure aarch64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: Version:3.4.0
WARNING	2025-10-27 17:46:59	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
WARNING	2025-10-27 17:46:59	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
INFO	2025-10-27 17:46:59	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Oct 27 17:46:59 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1604321280