Class org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest

Tool returned:
0

Using GATK wrapper script /home/runner/work/gatk/gatk/build/install/gatk/bin/gatk
Running:
    /home/runner/work/gatk/gatk/build/install/gatk/bin/gatk SetNmMdAndUqTags -I /dev/stdin -O /tmp/testOutput843817009600580658.bam --CREATE_INDEX true -R /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta
Using GATK wrapper script /home/runner/work/gatk/gatk/build/install/gatk/bin/gatk
Running:
    /home/runner/work/gatk/gatk/build/install/gatk/bin/gatk SortSam -I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.bam -O /dev/stdout -SO coordinate
20:33:56.065 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/work/gatk/gatk/build/install/gatk/lib/gkl-0.9.0.jar!/com/intel/gkl/native/libgkl_compression.so
20:33:56.066 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/work/gatk/gatk/build/install/gatk/lib/gkl-0.9.0.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu Jun 12 20:33:56 UTC 2025] SetNmMdAndUqTags --INPUT /dev/stdin --OUTPUT /tmp/testOutput843817009600580658.bam --CREATE_INDEX true --REFERENCE_SEQUENCE /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --IS_BISULFITE_SEQUENCE false --SET_ONLY_UQ false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Jun 12 20:33:56 UTC 2025] SortSam --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.bam --OUTPUT /dev/stdout --SORT_ORDER coordinate --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --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 20:33:56 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
[Thu Jun 12 20:33:56 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 20:33:56	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///dev/stdout
INFO	2025-06-12 20:33:56	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Jun 12 20:33:56 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=125829120
[Thu Jun 12 20:33:56 UTC 2025] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=146800640