Class org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSparkIntegrationTest

all > org.broadinstitute.hellbender.tools.spark.pathseq > PathSeqPipelineSparkIntegrationTest
2

tests
0

failures
0

ignored
3.408s

duration
100%

successful

Tests

Test Duration Result
testPipelineTool[0](pipeline_input.bam, pipeline_output.bam, pipeline_output.txt, pipeline_output.filter.metrics, pipeline_output.score.metrics, false) 2.084s passed
testPipelineTool[1](pipeline_input_aligned.bam, pipeline_output_aligned.bam, pipeline_output_aligned.txt, pipeline_output_aligned.filter.metrics, pipeline_output_aligned.score.metrics, true) 1.324s passed

Standard error

[June 12, 2025 at 8:59:33 PM GMT] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=754974720
[Thu Jun 12 20:59:33 GMT 2025] SortSam --INPUT /tmp/local18970223784451453307/pathseqPipelineTestOutput17804191120874252717.bam --OUTPUT /tmp/local18970223784451453307/resultsFileSorted2998068407207261168.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY STRICT --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
[Thu Jun 12 20:59:33 GMT 2025] Executing as root@e24cea241624 on Linux 6.11.0-1015-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:092bdf2-SNAPSHOT
INFO	2025-06-12 20:59:33	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Jun 12 20:59:33 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=754974720
[Thu Jun 12 20:59:33 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark/pipeline_output.bam --OUTPUT /tmp/local18970223784451453307/expectedFileSorted11207841692194853606.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY STRICT --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
[Thu Jun 12 20:59:33 GMT 2025] Executing as root@e24cea241624 on Linux 6.11.0-1015-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:092bdf2-SNAPSHOT
INFO	2025-06-12 20:59:33	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Jun 12 20:59:33 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=754974720
[June 12, 2025 at 8:59:34 PM GMT] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=754974720
[Thu Jun 12 20:59:34 GMT 2025] SortSam --INPUT /tmp/local18970223784451453307/pathseqPipelineTestOutput14382683521263612591.bam --OUTPUT /tmp/local18970223784451453307/resultsFileSorted3524298517190709927.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY STRICT --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
[Thu Jun 12 20:59:34 GMT 2025] Executing as root@e24cea241624 on Linux 6.11.0-1015-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:092bdf2-SNAPSHOT
INFO	2025-06-12 20:59:34	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Jun 12 20:59:34 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=754974720
[Thu Jun 12 20:59:34 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark/pipeline_output_aligned.bam --OUTPUT /tmp/local18970223784451453307/expectedFileSorted3113304226754053305.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY STRICT --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
[Thu Jun 12 20:59:34 GMT 2025] Executing as root@e24cea241624 on Linux 6.11.0-1015-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:092bdf2-SNAPSHOT
INFO	2025-06-12 20:59:34	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Jun 12 20:59:34 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=754974720