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

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

tests
0

failures
0

ignored
3.449s

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) 2.073s 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) 1.376s passed

Standard error

[May 27, 2025 at 2:57:12 PM UTC] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=2013265920
[Tue May 27 14:57:12 UTC 2025] SortSam --INPUT /tmp/local111378223953060423084/pathseqPipelineTestOutput13988060466977400983.bam --OUTPUT /tmp/local111378223953060423084/resultsFileSorted16407066221721254014.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 14:57:12 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 14:57:12	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 14:57:12 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2013265920
[Tue May 27 14:57:12 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark/pipeline_output.bam --OUTPUT /tmp/local111378223953060423084/expectedFileSorted8462096309647931079.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 14:57:12 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 14:57:12	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 14:57:12 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2013265920
[May 27, 2025 at 2:57:13 PM UTC] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2013265920
[Tue May 27 14:57:13 UTC 2025] SortSam --INPUT /tmp/local111378223953060423084/pathseqPipelineTestOutput15711822154359618903.bam --OUTPUT /tmp/local111378223953060423084/resultsFileSorted14562455059883037177.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 14:57:13 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 14:57:13	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 14:57:13 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2013265920
[Tue May 27 14:57:13 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark/pipeline_output_aligned.bam --OUTPUT /tmp/local111378223953060423084/expectedFileSorted5894425292191930548.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 14:57:13 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 14:57:13	SortSam	Finished reading inputs, merging and writing to output now.
[Tue May 27 14:57:13 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2013265920