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

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

tests
0

failures
0

ignored
5.450s

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')) 2.311s 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')) 1.215s 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 4:49:28 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=931135488
[Tue May 27 16:49:28 GMT 2025] SortSam --INPUT /tmp/local17251393156006128657/bqsrSparkPipelineTest7191510332432673117.bam --OUTPUT /tmp/local17251393156006128657/resultsFileSorted8843354980635310202.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 16:49:28 GMT 2025] Executing as root@1c4c36ffc4f6 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:113e5d7-SNAPSHOT
INFO	2025-05-27 16:49:28	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 16:49:28 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=931135488
[Tue May 27 16:49:28 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/local17251393156006128657/expectedFileSorted15995132755039358005.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 16:49:28 GMT 2025] Executing as root@1c4c36ffc4f6 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:113e5d7-SNAPSHOT
INFO	2025-05-27 16:49:28	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 16:49:28 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=931135488
[May 27, 2025 at 4:49:29 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=931135488
[Tue May 27 16:49:29 GMT 2025] SortSam --INPUT /tmp/local17251393156006128657/bqsrSparkPipelineTest9422094043742608357.bam --OUTPUT /tmp/local17251393156006128657/resultsFileSorted8612226546302986474.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 16:49:29 GMT 2025] Executing as root@1c4c36ffc4f6 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:113e5d7-SNAPSHOT
INFO	2025-05-27 16:49:29	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 16:49:29 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=931135488
[Tue May 27 16:49:29 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.bam --OUTPUT /tmp/local17251393156006128657/expectedFileSorted16655283386295501422.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 16:49:29 GMT 2025] Executing as root@1c4c36ffc4f6 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:113e5d7-SNAPSHOT
INFO	2025-05-27 16:49:29	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 16:49:29 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=931135488
[May 27, 2025 at 4:49:31 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1702887424
[Tue May 27 16:49:31 GMT 2025] SortSam --INPUT /tmp/local17251393156006128657/bqsrSparkPipelineTest4272414094206730253.cram --OUTPUT /tmp/local17251393156006128657/resultsFileSorted14942720364700455428.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 16:49:31 GMT 2025] Executing as root@1c4c36ffc4f6 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:113e5d7-SNAPSHOT
INFO	2025-05-27 16:49:31	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 16:49:31 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1702887424
[Tue May 27 16:49:31 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.cram --OUTPUT /tmp/local17251393156006128657/expectedFileSorted6185052638808482322.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 16:49:31 GMT 2025] Executing as root@1c4c36ffc4f6 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:113e5d7-SNAPSHOT
WARNING	2025-05-27 16:49:31	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
WARNING	2025-05-27 16:49:31	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
INFO	2025-05-27 16:49:31	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 16:49:31 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1702887424