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

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

tests
0

failures
0

ignored
3.570s

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) 2.137s 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) 1.433s passed

Standard error

[June 12, 2025 at 8:45:08 PM UTC] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1254096896
[Thu Jun 12 20:45:08 UTC 2025] SortSam --INPUT /tmp/local13085480587404488327/pathseqPipelineTestOutput17140883064443852321.bam --OUTPUT /tmp/local13085480587404488327/resultsFileSorted4740587199682815461.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 20:45:08 UTC 2025] Executing as runner@pkrvmxyh4eaekms on Linux 6.11.0-1015-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	2025-06-12 20:45:08	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Jun 12 20:45:08 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1254096896
[Thu Jun 12 20:45:08 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark/pipeline_output.bam --OUTPUT /tmp/local13085480587404488327/expectedFileSorted1736296856640999780.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 20:45:08 UTC 2025] Executing as runner@pkrvmxyh4eaekms on Linux 6.11.0-1015-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	2025-06-12 20:45:08	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Jun 12 20:45:08 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1254096896
[June 12, 2025 at 8:45:09 PM UTC] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1254096896
[Thu Jun 12 20:45:09 UTC 2025] SortSam --INPUT /tmp/local13085480587404488327/pathseqPipelineTestOutput2917340760227796141.bam --OUTPUT /tmp/local13085480587404488327/resultsFileSorted7366846009421778404.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 20:45:09 UTC 2025] Executing as runner@pkrvmxyh4eaekms on Linux 6.11.0-1015-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	2025-06-12 20:45:09	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Jun 12 20:45:10 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1254096896
[Thu Jun 12 20:45:10 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/local13085480587404488327/expectedFileSorted18135671994771325089.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 20:45:10 UTC 2025] Executing as runner@pkrvmxyh4eaekms on Linux 6.11.0-1015-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	2025-06-12 20:45:10	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Jun 12 20:45:10 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1254096896