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

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

tests
0

failures
0

ignored
5.207s

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')) 2.218s 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')) 1.181s 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')) 1.808s passed

Standard error

[May 27, 2025 at 3:45:06 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1501560832
[Tue May 27 15:45:06 UTC 2025] SortSam --INPUT /tmp/local15669066122832454348/bqsrSparkPipelineTest2684462301683582027.bam --OUTPUT /tmp/local15669066122832454348/resultsFileSorted18278740796012678057.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
[Tue May 27 15:45:06 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
INFO	2025-05-27 15:45:06	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 15:45:06 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1501560832
[Tue May 27 15:45:06 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/local15669066122832454348/expectedFileSorted13478479187052955450.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
[Tue May 27 15:45:06 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
INFO	2025-05-27 15:45:06	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 15:45:06 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1501560832
[May 27, 2025 at 3:45:07 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1501560832
[Tue May 27 15:45:07 UTC 2025] SortSam --INPUT /tmp/local15669066122832454348/bqsrSparkPipelineTest11764512036962951328.bam --OUTPUT /tmp/local15669066122832454348/resultsFileSorted4108874722925224052.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
[Tue May 27 15:45:07 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
INFO	2025-05-27 15:45:07	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 15:45:07 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1501560832
[Tue May 27 15:45:07 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.bam --OUTPUT /tmp/local15669066122832454348/expectedFileSorted9468417228477879748.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
[Tue May 27 15:45:07 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
INFO	2025-05-27 15:45:07	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 15:45:07 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1501560832
[May 27, 2025 at 3:45:08 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1505755136
[Tue May 27 15:45:08 UTC 2025] SortSam --INPUT /tmp/local15669066122832454348/bqsrSparkPipelineTest4290866298205411109.cram --OUTPUT /tmp/local15669066122832454348/resultsFileSorted8151811392651209628.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
[Tue May 27 15:45:08 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
INFO	2025-05-27 15:45:08	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 15:45:09 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1426063360
[Tue May 27 15:45:09 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.MultiSite.bqsr.pipeline.cram --OUTPUT /tmp/local15669066122832454348/expectedFileSorted3473722552367249794.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
[Tue May 27 15:45:09 UTC 2025] Executing as runner@pkrvmf6wy0o8zjz on Linux 6.11.0-1014-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.4.0
WARNING	2025-05-27 15:45:09	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
WARNING	2025-05-27 15:45:09	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
INFO	2025-05-27 15:45:09	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 15:45:09 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1426063360