Class org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalkerIntegrationTest

AAA Seen: 78 Reads 9 Variants 3
AAC Seen: 1 Reads 0 Variants 1
ACC Seen: 1 Reads 0 Variants 1
CCC Seen: 78 Reads 0 Variants 1
CCG Seen: 1 Reads 0 Variants 0
CGG Seen: 1 Reads 0 Variants 0
GGG Seen: 78 Reads 0 Variants 0
GGT Seen: 1 Reads 0 Variants 0
GTT Seen: 1 Reads 0 Variants 0
NAA Seen: 1 Reads 1 Variants 0
NN Seen: 1 Reads 0 Variants 0
NNA Seen: 1 Reads 1 Variants 0
NNN Seen: 78 Reads 1 Variants 0
TT Seen: 1 Reads 0 Variants 0
TTT Seen: 78 Reads 0 Variants 0

17:42:39.412 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:42:39.415 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression15220554105857495305.so: /tmp/libgkl_compression15220554105857495305.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:42:39.415 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:42:39.418 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression15742012383391746238.so: /tmp/libgkl_compression15742012383391746238.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:42:39.419 INFO  ExampleReferenceWalker - ------------------------------------------------------------
17:42:39.419 INFO  ExampleReferenceWalker - org.broadinstitute.hellbender.tools.examples vUnavailable
17:42:39.419 INFO  ExampleReferenceWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
17:42:39.419 INFO  ExampleReferenceWalker - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:42:39.419 INFO  ExampleReferenceWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:42:39.419 INFO  ExampleReferenceWalker - Start Date/Time: October 27, 2025 at 5:42:39 PM UTC
17:42:39.419 INFO  ExampleReferenceWalker - ------------------------------------------------------------
17:42:39.419 INFO  ExampleReferenceWalker - ------------------------------------------------------------
17:42:39.419 INFO  ExampleReferenceWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:42:39.420 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:42:39.420 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:42:39.420 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:42:39.420 INFO  ExampleReferenceWalker - Deflater: JdkDeflater
17:42:39.420 INFO  ExampleReferenceWalker - Inflater: JdkInflater
17:42:39.420 INFO  ExampleReferenceWalker - GCS max retries/reopens: 20
17:42:39.420 INFO  ExampleReferenceWalker - Requester pays: disabled
17:42:39.420 INFO  ExampleReferenceWalker - Initializing engine
17:42:39.421 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:39.421 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:42:39.422 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf
17:42:39.423 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
17:42:39.423 INFO  ExampleReferenceWalker - Done initializing engine
17:42:39.424 INFO  ProgressMeter - Starting traversal
17:42:39.424 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
17:42:39.431 INFO  ProgressMeter -             unmapped              0.0                   400        4000000.0
17:42:39.431 INFO  ProgressMeter - Traversal complete. Processed 400 total bases in 0.0 minutes.
17:42:39.431 INFO  ExampleReferenceWalker - Shutting down engine
[October 27, 2025 at 5:42:39 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2810183680