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

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

tests
0

failures
0

ignored
3.584s

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) 2.206s 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) 1.378s passed

Standard error

[May 27, 2025 at 6:31:10 PM GMT] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=987758592
[Tue May 27 18:31:10 GMT 2025] SortSam --INPUT /tmp/local13803678826696211271/pathseqPipelineTestOutput15474874166621645659.bam --OUTPUT /tmp/local13803678826696211271/resultsFileSorted1041745514277222373.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
[Tue May 27 18:31:10 GMT 2025] Executing as root@9bb9f17fa524 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:06789f4-SNAPSHOT
INFO	2025-05-27 18:31:10	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 18:31:10 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=987758592
[Tue May 27 18:31:10 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark/pipeline_output.bam --OUTPUT /tmp/local13803678826696211271/expectedFileSorted6136915187030325622.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
[Tue May 27 18:31:10 GMT 2025] Executing as root@9bb9f17fa524 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:06789f4-SNAPSHOT
INFO	2025-05-27 18:31:10	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 18:31:10 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=987758592
[May 27, 2025 at 6:31:11 PM GMT] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=987758592
[Tue May 27 18:31:11 GMT 2025] SortSam --INPUT /tmp/local13803678826696211271/pathseqPipelineTestOutput15435122932190950701.bam --OUTPUT /tmp/local13803678826696211271/resultsFileSorted6240063563643509938.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
[Tue May 27 18:31:11 GMT 2025] Executing as root@9bb9f17fa524 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:06789f4-SNAPSHOT
INFO	2025-05-27 18:31:11	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 18:31:11 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=987758592
[Tue May 27 18:31:11 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark/pipeline_output_aligned.bam --OUTPUT /tmp/local13803678826696211271/expectedFileSorted7004733694873401490.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
[Tue May 27 18:31:11 GMT 2025] Executing as root@9bb9f17fa524 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:06789f4-SNAPSHOT
INFO	2025-05-27 18:31:11	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 18:31:11 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=987758592