Class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariantsIntegrationTest
Tests
| Test |
Duration |
Result |
| testSampleSelectionOnNio |
2.420s |
passed |
Standard error
17:48:16.745 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
17:48:16.751 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression5382529196646288557.so: /tmp/libgkl_compression5382529196646288557.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:48:16.753 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
17:48:16.757 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4006518899412479411.so: /tmp/libgkl_compression4006518899412479411.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:48:16.760 INFO SelectVariants - ------------------------------------------------------------
17:48:16.763 INFO SelectVariants - org.broadinstitute.hellbender.tools.walkers.variantutils vUnavailable
17:48:16.763 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
17:48:16.763 INFO SelectVariants - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:48:16.763 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:48:16.763 INFO SelectVariants - Start Date/Time: October 27, 2025 at 5:48:16 PM UTC
17:48:16.763 INFO SelectVariants - ------------------------------------------------------------
17:48:16.764 INFO SelectVariants - ------------------------------------------------------------
17:48:16.764 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:48:16.764 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:48:16.764 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:48:16.764 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:48:16.765 INFO SelectVariants - Deflater: JdkDeflater
17:48:16.765 INFO SelectVariants - Inflater: JdkInflater
17:48:16.765 INFO SelectVariants - GCS max retries/reopens: 20
17:48:16.765 INFO SelectVariants - Requester pays: disabled
17:48:16.765 INFO SelectVariants - Initializing engine
17:48:16.783 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf
17:48:16.788 WARN IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
17:48:16.789 WARN IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
17:48:16.792 INFO SelectVariants - Done initializing engine
17:48:16.792 WARN SelectVariants - ***************************************************************************************************************************
17:48:16.793 WARN SelectVariants - * Detected unsorted genotype fields on input. *
17:48:16.793 WARN SelectVariants - * SelectVariants will sort the genotypes on output which could result in slow traversal as it involves genotype parsing. *
17:48:16.793 WARN SelectVariants - ***************************************************************************************************************************
17:48:16.799 INFO SelectVariants - Including sample 'NA11918'
17:48:16.801 WARN IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
17:48:17.476 INFO ProgressMeter - Starting traversal
17:48:17.476 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
17:48:17.491 INFO ProgressMeter - unmapped 0.0 14 60000.0
17:48:17.491 INFO ProgressMeter - Traversal complete. Processed 14 total variants in 0.0 minutes.
17:48:18.142 INFO SelectVariants - Shutting down engine
[October 27, 2025 at 5:48:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=524288000