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

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

tests
0

failures
0

ignored
5.512s

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')) 2.433s 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')) 1.121s 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')) 1.958s passed

Standard error

[June 2, 2025 at 2:35:20 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=989855744
[Mon Jun 02 14:35:20 GMT 2025] SortSam --INPUT /tmp/local15649932464249107734/bqsrSparkPipelineTest1221906657832496859.bam --OUTPUT /tmp/local15649932464249107734/resultsFileSorted2777774822495674069.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
[Mon Jun 02 14:35:20 GMT 2025] Executing as root@7f71e7f19701 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:5749ecb-SNAPSHOT
INFO	2025-06-02 14:35:20	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Jun 02 14:35:20 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[Mon Jun 02 14:35:20 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/local15649932464249107734/expectedFileSorted670371390056090712.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
[Mon Jun 02 14:35:20 GMT 2025] Executing as root@7f71e7f19701 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:5749ecb-SNAPSHOT
INFO	2025-06-02 14:35:20	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Jun 02 14:35:20 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[June 2, 2025 at 2:35:21 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=989855744
[Mon Jun 02 14:35:21 GMT 2025] SortSam --INPUT /tmp/local15649932464249107734/bqsrSparkPipelineTest824850381394682418.bam --OUTPUT /tmp/local15649932464249107734/resultsFileSorted1841981399641482054.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
[Mon Jun 02 14:35:21 GMT 2025] Executing as root@7f71e7f19701 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:5749ecb-SNAPSHOT
INFO	2025-06-02 14:35:21	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Jun 02 14:35:21 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[Mon Jun 02 14:35:21 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.bam --OUTPUT /tmp/local15649932464249107734/expectedFileSorted11988236194535222837.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
[Mon Jun 02 14:35:21 GMT 2025] Executing as root@7f71e7f19701 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:5749ecb-SNAPSHOT
INFO	2025-06-02 14:35:21	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Jun 02 14:35:21 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[June 2, 2025 at 2:35:23 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1054867456
[Mon Jun 02 14:35:23 GMT 2025] SortSam --INPUT /tmp/local15649932464249107734/bqsrSparkPipelineTest7152321104101372704.cram --OUTPUT /tmp/local15649932464249107734/resultsFileSorted3218256083237349024.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
[Mon Jun 02 14:35:23 GMT 2025] Executing as root@7f71e7f19701 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:5749ecb-SNAPSHOT
INFO	2025-06-02 14:35:23	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Jun 02 14:35:23 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1054867456
[Mon Jun 02 14:35:23 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.cram --OUTPUT /tmp/local15649932464249107734/expectedFileSorted14886246132333545077.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
[Mon Jun 02 14:35:23 GMT 2025] Executing as root@7f71e7f19701 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:5749ecb-SNAPSHOT
WARNING	2025-06-02 14:35:23	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
WARNING	2025-06-02 14:35:23	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
INFO	2025-06-02 14:35:23	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Jun 02 14:35:23 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1054867456