Class org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest

Tool returned:
0

Using GATK jar /gatk/gatk-package-092bdf2-SNAPSHOT-local.jar
Running:
Using GATK jar /gatk/gatk-package-092bdf2-SNAPSHOT-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-092bdf2-SNAPSHOT-local.jar SetNmMdAndUqTags -I /dev/stdin -O /tmp/testOutput12073697886199631652.bam --CREATE_INDEX true -R /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-092bdf2-SNAPSHOT-local.jar SortSam -I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.bam -O /dev/stdout -SO coordinate
20:48:01.569 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-092bdf2-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
20:48:01.594 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-092bdf2-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu Jun 12 20:48:01 GMT 2025] SortSam --INPUT /gatkCloneMountPoint/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 20:48:01 GMT 2025] SetNmMdAndUqTags --INPUT /dev/stdin --OUTPUT /tmp/testOutput12073697886199631652.bam --CREATE_INDEX true --REFERENCE_SEQUENCE /gatkCloneMountPoint/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 20:48:01 GMT 2025] Executing as root@e24cea241624 on Linux 6.11.0-1015-azure amd64; OpenJDK 64-Bit Server VM 17.0.12+7-Ubuntu-1ubuntu222.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:092bdf2-SNAPSHOT
INFO	2025-06-12 20:48:01	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///dev/stdout
[Thu Jun 12 20:48:01 GMT 2025] Executing as root@e24cea241624 on Linux 6.11.0-1015-azure amd64; OpenJDK 64-Bit Server VM 17.0.12+7-Ubuntu-1ubuntu222.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:092bdf2-SNAPSHOT
INFO	2025-06-12 20:48:01	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Jun 12 20:48:01 GMT 2025] picard.sam.SortSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=119537664
[Thu Jun 12 20:48:02 GMT 2025] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=169869312