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')) |
2.170s |
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')) |
1.050s |
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')) |
1.963s |
passed |
Standard error
[May 27, 2025 at 4:00:03 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1006632960
[Tue May 27 16:00:03 GMT 2025] SortSam --INPUT /tmp/local116905632234052656723/bqsrSparkPipelineTest5951750948591008891.bam --OUTPUT /tmp/local116905632234052656723/resultsFileSorted13263794129502035890.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 16:00:03 GMT 2025] Executing as root@1be272c3efa7 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:f5385f1-SNAPSHOT
INFO 2025-05-27 16:00:03 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 16:00:03 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1006632960
[Tue May 27 16:00:03 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/local116905632234052656723/expectedFileSorted3836102121514415062.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 16:00:03 GMT 2025] Executing as root@1be272c3efa7 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:f5385f1-SNAPSHOT
INFO 2025-05-27 16:00:03 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 16:00:03 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1006632960
[May 27, 2025 at 4:00:04 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1006632960
[Tue May 27 16:00:04 GMT 2025] SortSam --INPUT /tmp/local116905632234052656723/bqsrSparkPipelineTest4974449476170446906.bam --OUTPUT /tmp/local116905632234052656723/resultsFileSorted5633048648302544609.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 16:00:04 GMT 2025] Executing as root@1be272c3efa7 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:f5385f1-SNAPSHOT
INFO 2025-05-27 16:00:04 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 16:00:04 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1006632960
[Tue May 27 16:00:04 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.bam --OUTPUT /tmp/local116905632234052656723/expectedFileSorted9372807764951494204.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 16:00:04 GMT 2025] Executing as root@1be272c3efa7 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:f5385f1-SNAPSHOT
INFO 2025-05-27 16:00:04 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 16:00:04 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1006632960
[May 27, 2025 at 4:00:06 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1071644672
[Tue May 27 16:00:06 GMT 2025] SortSam --INPUT /tmp/local116905632234052656723/bqsrSparkPipelineTest13786493893569042639.cram --OUTPUT /tmp/local116905632234052656723/resultsFileSorted246113549890955629.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 16:00:06 GMT 2025] Executing as root@1be272c3efa7 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:f5385f1-SNAPSHOT
INFO 2025-05-27 16:00:06 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 16:00:06 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1784676352
[Tue May 27 16:00:06 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.cram --OUTPUT /tmp/local116905632234052656723/expectedFileSorted4343067045168817157.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 16:00:06 GMT 2025] Executing as root@1be272c3efa7 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:f5385f1-SNAPSHOT
WARNING 2025-05-27 16:00:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN
WARNING 2025-05-27 16:00:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC
INFO 2025-05-27 16:00:06 SortSam Finished reading inputs, merging and writing to output now.
[Tue May 27 16:00:06 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1784676352