Class org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest

Tool returned:
0

Using GATK wrapper script /home/runner/work/gatk/gatk/build/install/gatk/bin/gatk
Running:
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/testOutput18257437943597522748.bam --CREATE_INDEX true -R /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta
    /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
17:38:37.702 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/work/gatk/gatk/build/install/gatk/lib/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:38:37.707 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/work/gatk/gatk/build/install/gatk/lib/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:38:37.738 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/runner/libgkl_compression15667129694272914165.so: /tmp/runner/libgkl_compression15667129694272914165.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:38:37.740 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/runner/libgkl_compression2354298800608869001.so: /tmp/runner/libgkl_compression2354298800608869001.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:38:37.740 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/work/gatk/gatk/build/install/gatk/lib/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:38:37.742 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/work/gatk/gatk/build/install/gatk/lib/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:38:37.745 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/runner/libgkl_compression5218006441975299777.so: /tmp/runner/libgkl_compression5218006441975299777.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:38:37.745 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/runner/libgkl_compression17418067864917580875.so: /tmp/runner/libgkl_compression17418067864917580875.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
[Mon Oct 27 17:38:37 UTC 2025] SetNmMdAndUqTags --INPUT /dev/stdin --OUTPUT /tmp/testOutput18257437943597522748.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
[Mon Oct 27 17:38:37 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
[Mon Oct 27 17:38:37 UTC 2025] Executing as runner@runnervmrcw8b on Linux 6.11.0-1018-azure aarch64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: Version:3.4.0
[Mon Oct 27 17:38:37 UTC 2025] Executing as runner@runnervmrcw8b on Linux 6.11.0-1018-azure aarch64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: Version:3.4.0
17:38:37.895 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:38:37.899 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
INFO	2025-10-27 17:38:37	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///dev/stdout
17:38:37.919 WARN  IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
INFO	2025-10-27 17:38:37	SortSam	Finished reading inputs, merging and writing to output now.
[Mon Oct 27 17:38:38 UTC 2025] picard.sam.SortSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=125829120
17:38:38.035 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:38:38.038 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:38:38.041 WARN  IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
[Mon Oct 27 17:38:38 UTC 2025] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=239075328