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

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

tests
0

failures
0

ignored
3.402s

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) 2.034s 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) 1.368s passed

Standard error

[June 2, 2025 at 2:35:11 PM GMT] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=989855744
[Mon Jun 02 14:35:11 GMT 2025] SortSam --INPUT /tmp/local15649932464249107734/pathseqPipelineTestOutput5965619537796720761.bam --OUTPUT /tmp/local15649932464249107734/resultsFileSorted11973130586058440652.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
[Mon Jun 02 14:35:11 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 14:35:11	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Jun 02 14:35:11 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[Mon Jun 02 14:35:11 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark/pipeline_output.bam --OUTPUT /tmp/local15649932464249107734/expectedFileSorted3315887817424152788.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
[Mon Jun 02 14:35:11 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 14:35:11	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Jun 02 14:35:11 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[June 2, 2025 at 2:35:12 PM GMT] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=989855744
[Mon Jun 02 14:35:12 GMT 2025] SortSam --INPUT /tmp/local15649932464249107734/pathseqPipelineTestOutput1370008351730851215.bam --OUTPUT /tmp/local15649932464249107734/resultsFileSorted6754928578353695285.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
[Mon Jun 02 14:35:12 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 14:35:12	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Jun 02 14:35:13 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[Mon Jun 02 14:35:13 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark/pipeline_output_aligned.bam --OUTPUT /tmp/local15649932464249107734/expectedFileSorted7083038431180206200.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
[Mon Jun 02 14:35:13 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 14:35:13	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Jun 02 14:35:13 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744