Class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariantsIntegrationTest

22:48:41.527 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.8.11/13f95ee601084b8bf047b2a37f6ea36cd588b96b/gkl-0.8.11.jar!/com/intel/gkl/native/libgkl_compression.so
22:48:41.538 INFO  SelectVariants - ------------------------------------------------------------
22:48:41.541 INFO  SelectVariants - org.broadinstitute.hellbender.tools.walkers.variantutils vUnavailable
22:48:41.541 INFO  SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
22:48:41.541 INFO  SelectVariants - Executing as runner@fv-az2219-44 on Linux v6.8.0-1021-azure amd64
22:48:41.541 INFO  SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:48:41.541 INFO  SelectVariants - Start Date/Time: March 28, 2025 at 10:48:41 PM UTC
22:48:41.541 INFO  SelectVariants - ------------------------------------------------------------
22:48:41.542 INFO  SelectVariants - ------------------------------------------------------------
22:48:41.542 INFO  SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:48:41.542 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:48:41.543 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:48:41.543 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:48:41.543 INFO  SelectVariants - Deflater: IntelDeflater
22:48:41.543 INFO  SelectVariants - Inflater: IntelInflater
22:48:41.543 INFO  SelectVariants - GCS max retries/reopens: 20
22:48:41.543 INFO  SelectVariants - Requester pays: disabled
22:48:41.544 INFO  SelectVariants - Initializing engine
22:48:41.561 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
22:48:41.569 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
22:48:41.570 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
22:48:41.572 INFO  SelectVariants - Done initializing engine
22:48:41.573 WARN  SelectVariants - ***************************************************************************************************************************
22:48:41.573 WARN  SelectVariants - * Detected unsorted genotype fields on input.                                                                             *
22:48:41.573 WARN  SelectVariants - * SelectVariants will sort the genotypes on output which could result in slow traversal as it involves genotype parsing.  *
22:48:41.573 WARN  SelectVariants - ***************************************************************************************************************************
22:48:41.583 INFO  SelectVariants - Including sample 'NA11918'
22:48:41.585 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
22:48:42.602 INFO  ProgressMeter - Starting traversal
22:48:42.602 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:48:42.624 INFO  ProgressMeter -             unmapped              0.0                    14          40000.0
22:48:42.625 INFO  ProgressMeter - Traversal complete. Processed 14 total variants in 0.0 minutes.
22:48:44.091 INFO  SelectVariants - Shutting down engine
[March 28, 2025 at 10:48:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=524288000