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

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

tests
0

failures
0

ignored
5.664s

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')) 2.511s 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')) 1.188s 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')) 1.965s passed

Standard error

[March 28, 2025 at 10:44:44 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1149239296
[Fri Mar 28 22:44:44 UTC 2025] SortSam --INPUT /tmp/local116208583777069067979/bqsrSparkPipelineTest8621007175073403682.bam --OUTPUT /tmp/local116208583777069067979/resultsFileSorted13460797488641851173.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
[Fri Mar 28 22:44:44 UTC 2025] Executing as runner@fv-az1690-153 on Linux 6.8.0-1021-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
INFO	2025-03-28 22:44:44	SortSam	Finished reading inputs, merging and writing to output now.
[Fri Mar 28 22:44:44 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1149239296
[Fri Mar 28 22:44:44 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/local116208583777069067979/expectedFileSorted3613078168584432984.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
[Fri Mar 28 22:44:44 UTC 2025] Executing as runner@fv-az1690-153 on Linux 6.8.0-1021-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
INFO	2025-03-28 22:44:44	SortSam	Finished reading inputs, merging and writing to output now.
[Fri Mar 28 22:44:44 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1149239296
[March 28, 2025 at 10:44:46 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1149239296
[Fri Mar 28 22:44:46 UTC 2025] SortSam --INPUT /tmp/local116208583777069067979/bqsrSparkPipelineTest425081614269362568.bam --OUTPUT /tmp/local116208583777069067979/resultsFileSorted7239032735424216857.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
[Fri Mar 28 22:44:46 UTC 2025] Executing as runner@fv-az1690-153 on Linux 6.8.0-1021-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
INFO	2025-03-28 22:44:46	SortSam	Finished reading inputs, merging and writing to output now.
[Fri Mar 28 22:44:46 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1149239296
[Fri Mar 28 22:44:46 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.bam --OUTPUT /tmp/local116208583777069067979/expectedFileSorted7245315587357452619.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
[Fri Mar 28 22:44:46 UTC 2025] Executing as runner@fv-az1690-153 on Linux 6.8.0-1021-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
INFO	2025-03-28 22:44:46	SortSam	Finished reading inputs, merging and writing to output now.
[Fri Mar 28 22:44:46 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1149239296
[March 28, 2025 at 10:44:47 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1277165568
[Fri Mar 28 22:44:47 UTC 2025] SortSam --INPUT /tmp/local116208583777069067979/bqsrSparkPipelineTest11776276466042781735.cram --OUTPUT /tmp/local116208583777069067979/resultsFileSorted2277105766555199961.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
[Fri Mar 28 22:44:47 UTC 2025] Executing as runner@fv-az1690-153 on Linux 6.8.0-1021-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
INFO	2025-03-28 22:44:47	SortSam	Finished reading inputs, merging and writing to output now.
[Fri Mar 28 22:44:47 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1390411776
[Fri Mar 28 22:44:47 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.cram --OUTPUT /tmp/local116208583777069067979/expectedFileSorted14867381837335047251.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
[Fri Mar 28 22:44:47 UTC 2025] Executing as runner@fv-az1690-153 on Linux 6.8.0-1021-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
WARNING	2025-03-28 22:44:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
WARNING	2025-03-28 22:44:47	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
INFO	2025-03-28 22:44:47	SortSam	Finished reading inputs, merging and writing to output now.
[Fri Mar 28 22:44:48 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1390411776