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')) |
2.537s |
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')) |
1.157s |
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')) |
1.937s |
passed |
Standard error
[May 27, 2025 at 2:04:33 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=950009856
[Tue May 27 14:04:33 GMT 2025] SortSam --INPUT /tmp/local111892862105095196395/bqsrSparkPipelineTest8641619054838605585.bam --OUTPUT /tmp/local111892862105095196395/resultsFileSorted13663036867168072872.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /gatkCloneMountPoint/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 14:04:33 GMT 2025] Executing as root@9cd1444b9593 on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.12+7-Ubuntu-1ubuntu222.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:5c95f6f-SNAPSHOT
INFO 2025-05-27 14:04:33 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 14:04:33 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=950009856
[Tue May 27 14:04:33 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recalibrated.DIQ.bam --OUTPUT /tmp/local111892862105095196395/expectedFileSorted260719170271969048.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /gatkCloneMountPoint/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 14:04:33 GMT 2025] Executing as root@9cd1444b9593 on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.12+7-Ubuntu-1ubuntu222.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:5c95f6f-SNAPSHOT
INFO 2025-05-27 14:04:33 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 14:04:33 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=950009856
[May 27, 2025 at 2:04:34 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=950009856
[Tue May 27 14:04:34 GMT 2025] SortSam --INPUT /tmp/local111892862105095196395/bqsrSparkPipelineTest16755077769259225897.bam --OUTPUT /tmp/local111892862105095196395/resultsFileSorted6174903495623057181.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /gatkCloneMountPoint/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 14:04:34 GMT 2025] Executing as root@9cd1444b9593 on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.12+7-Ubuntu-1ubuntu222.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:5c95f6f-SNAPSHOT
INFO 2025-05-27 14:04:34 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 14:04:34 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=950009856
[Tue May 27 14:04:34 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.bam --OUTPUT /tmp/local111892862105095196395/expectedFileSorted4138500267307388564.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /gatkCloneMountPoint/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 14:04:34 GMT 2025] Executing as root@9cd1444b9593 on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.12+7-Ubuntu-1ubuntu222.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:5c95f6f-SNAPSHOT
INFO 2025-05-27 14:04:34 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 14:04:34 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=950009856
[May 27, 2025 at 2:04:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1025507328
[Tue May 27 14:04:35 GMT 2025] SortSam --INPUT /tmp/local111892862105095196395/bqsrSparkPipelineTest14132935886079100229.cram --OUTPUT /tmp/local111892862105095196395/resultsFileSorted12797818875030772699.cram --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /gatkCloneMountPoint/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 14:04:35 GMT 2025] Executing as root@9cd1444b9593 on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.12+7-Ubuntu-1ubuntu222.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:5c95f6f-SNAPSHOT
INFO 2025-05-27 14:04:36 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 14:04:36 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1025507328
[Tue May 27 14:04:36 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.cram --OUTPUT /tmp/local111892862105095196395/expectedFileSorted2800674163071386720.cram --SORT_ORDER coordinate --VALIDATION_STRINGENCY SILENT --REFERENCE_SEQUENCE /gatkCloneMountPoint/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 14:04:36 GMT 2025] Executing as root@9cd1444b9593 on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.12+7-Ubuntu-1ubuntu222.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:5c95f6f-SNAPSHOT
WARNING 2025-05-27 14:04:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN
WARNING 2025-05-27 14:04:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC
INFO 2025-05-27 14:04:36 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 14:04:36 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808