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

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

tests
0

failures
0

ignored
3.494s

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) 2.091s 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) 1.403s passed

Standard error

[May 19, 2025 at 6:58:57 PM UTC] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1065353216
[Mon May 19 18:58:57 UTC 2025] SortSam --INPUT /tmp/local12542579939630629552/pathseqPipelineTestOutput1626459552388710623.bam --OUTPUT /tmp/local12542579939630629552/resultsFileSorted5913462156924052379.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 May 19 18:58:57 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	2025-05-19 18:58:57	SortSam	Finished reading inputs, merging and writing to output now.
[Mon May 19 18:58:57 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1065353216
[Mon May 19 18:58:57 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark/pipeline_output.bam --OUTPUT /tmp/local12542579939630629552/expectedFileSorted502174597232766644.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 May 19 18:58:57 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	2025-05-19 18:58:57	SortSam	Finished reading inputs, merging and writing to output now.
[Mon May 19 18:58:57 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1065353216
[May 19, 2025 at 6:58:58 PM UTC] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1587544064
[Mon May 19 18:58:58 UTC 2025] SortSam --INPUT /tmp/local12542579939630629552/pathseqPipelineTestOutput6744620900359508540.bam --OUTPUT /tmp/local12542579939630629552/resultsFileSorted17660379931298269871.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 May 19 18:58:58 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	2025-05-19 18:58:58	SortSam	Finished reading inputs, merging and writing to output now.
[Mon May 19 18:58:58 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1587544064
[Mon May 19 18:58:58 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/local12542579939630629552/expectedFileSorted8188917556750336845.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 May 19 18:58:58 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	2025-05-19 18:58:58	SortSam	Finished reading inputs, merging and writing to output now.
[Mon May 19 18:58:58 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1587544064