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

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

tests
0

failures
0

ignored
3.476s

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) 2.152s 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) 1.324s passed

Standard error

[March 28, 2025 at 10:44:35 PM UTC] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=524288000
[Fri Mar 28 22:44:35 UTC 2025] SortSam --INPUT /tmp/local116208583777069067979/pathseqPipelineTestOutput6833542806024975633.bam --OUTPUT /tmp/local116208583777069067979/resultsFileSorted3710342092048001732.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
[Fri Mar 28 22:44:35 UTC 2025] Executing as runner@fv-az1690-153 on Linux 6.8.0-1021-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
INFO	2025-03-28 22:44:35	SortSam	Finished reading inputs, merging and writing to output now.
[Fri Mar 28 22:44:35 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[Fri Mar 28 22:44:35 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark/pipeline_output.bam --OUTPUT /tmp/local116208583777069067979/expectedFileSorted14685186554988024389.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
[Fri Mar 28 22:44:35 UTC 2025] Executing as runner@fv-az1690-153 on Linux 6.8.0-1021-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
INFO	2025-03-28 22:44:35	SortSam	Finished reading inputs, merging and writing to output now.
[Fri Mar 28 22:44:35 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:44:37 PM UTC] org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=524288000
[Fri Mar 28 22:44:37 UTC 2025] SortSam --INPUT /tmp/local116208583777069067979/pathseqPipelineTestOutput10694966978304964894.bam --OUTPUT /tmp/local116208583777069067979/resultsFileSorted1372504668190537730.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
[Fri Mar 28 22:44:37 UTC 2025] Executing as runner@fv-az1690-153 on Linux 6.8.0-1021-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
INFO	2025-03-28 22:44:37	SortSam	Finished reading inputs, merging and writing to output now.
[Fri Mar 28 22:44:37 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[Fri Mar 28 22:44:37 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/local116208583777069067979/expectedFileSorted377138588925225073.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
[Fri Mar 28 22:44:37 UTC 2025] Executing as runner@fv-az1690-153 on Linux 6.8.0-1021-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
INFO	2025-03-28 22:44:37	SortSam	Finished reading inputs, merging and writing to output now.
[Fri Mar 28 22:44:37 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000