Class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariantsIntegrationTest
Tests
| Test |
Duration |
Result |
| testSampleSelectionOnNio |
2.725s |
passed |
Standard error
20:51:32.387 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.0/5ec646c7bf8c4f7681c2a59819384e5da469db31/gkl-0.9.0.jar!/com/intel/gkl/native/libgkl_compression.so
20:51:32.398 INFO SelectVariants - ------------------------------------------------------------
20:51:32.402 INFO SelectVariants - org.broadinstitute.hellbender.tools.walkers.variantutils vUnavailable
20:51:32.402 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
20:51:32.402 INFO SelectVariants - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:51:32.402 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:51:32.402 INFO SelectVariants - Start Date/Time: June 12, 2025 at 8:51:32 PM UTC
20:51:32.402 INFO SelectVariants - ------------------------------------------------------------
20:51:32.403 INFO SelectVariants - ------------------------------------------------------------
20:51:32.403 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:51:32.403 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:51:32.403 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:51:32.404 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:51:32.404 INFO SelectVariants - Deflater: IntelDeflater
20:51:32.404 INFO SelectVariants - Inflater: IntelInflater
20:51:32.404 INFO SelectVariants - GCS max retries/reopens: 20
20:51:32.404 INFO SelectVariants - Requester pays: disabled
20:51:32.405 INFO SelectVariants - Initializing engine
20:51:32.422 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
20:51:32.429 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
20:51:32.430 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
20:51:32.433 INFO SelectVariants - Done initializing engine
20:51:32.434 WARN SelectVariants - ***************************************************************************************************************************
20:51:32.434 WARN SelectVariants - * Detected unsorted genotype fields on input. *
20:51:32.434 WARN SelectVariants - * SelectVariants will sort the genotypes on output which could result in slow traversal as it involves genotype parsing. *
20:51:32.434 WARN SelectVariants - ***************************************************************************************************************************
20:51:32.443 INFO SelectVariants - Including sample 'NA11918'
20:51:32.445 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
20:51:33.215 INFO ProgressMeter - Starting traversal
20:51:33.216 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:51:33.237 INFO ProgressMeter - unmapped 0.0 14 40000.0
20:51:33.237 INFO ProgressMeter - Traversal complete. Processed 14 total variants in 0.0 minutes.
20:51:33.934 INFO SelectVariants - Shutting down engine
[June 12, 2025 at 8:51:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=524288000