Class org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSparkIntegrationTest
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')) |
2.320s |
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')) |
1.223s |
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')) |
1.924s |
passed |
Standard error
[May 27, 2025 at 1:49:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1681915904
[Tue May 27 13:49:23 UTC 2025] SortSam --INPUT /tmp/local15243704403060221796/bqsrSparkPipelineTest7789911968844807677.bam --OUTPUT /tmp/local15243704403060221796/resultsFileSorted15639046213033838432.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
[Tue May 27 13:49:23 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
INFO 2025-05-27 13:49:23 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 13:49:23 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1681915904
[Tue May 27 13:49:23 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/local15243704403060221796/expectedFileSorted4399215762527805033.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
[Tue May 27 13:49:23 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
INFO 2025-05-27 13:49:23 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 13:49:23 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1681915904
[May 27, 2025 at 1:49:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1681915904
[Tue May 27 13:49:24 UTC 2025] SortSam --INPUT /tmp/local15243704403060221796/bqsrSparkPipelineTest3126992297645209125.bam --OUTPUT /tmp/local15243704403060221796/resultsFileSorted15953184559393127014.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
[Tue May 27 13:49:24 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
INFO 2025-05-27 13:49:24 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 13:49:24 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1681915904
[Tue May 27 13:49:24 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.bam --OUTPUT /tmp/local15243704403060221796/expectedFileSorted2250113674941521745.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
[Tue May 27 13:49:24 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
INFO 2025-05-27 13:49:24 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 13:49:24 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1681915904
[May 27, 2025 at 1:49:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1721761792
[Tue May 27 13:49:26 UTC 2025] SortSam --INPUT /tmp/local15243704403060221796/bqsrSparkPipelineTest16840389878768946829.cram --OUTPUT /tmp/local15243704403060221796/resultsFileSorted13435612309736064692.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
[Tue May 27 13:49:26 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
INFO 2025-05-27 13:49:26 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 13:49:26 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1721761792
[Tue May 27 13:49:26 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.cram --OUTPUT /tmp/local15243704403060221796/expectedFileSorted7824919021836077668.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
[Tue May 27 13:49:26 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
WARNING 2025-05-27 13:49:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN
WARNING 2025-05-27 13:49:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC
INFO 2025-05-27 13:49:26 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 13:49:26 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1835008000