Using GATK jar /mmfs1/gscratch/srlab/nextflow/bin/miniforge/envs/gatk4/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-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 /mmfs1/gscratch/srlab/nextflow/bin/miniforge/envs/gatk4/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar SelectVariants -R /gscratch/srlab/strigg/GENOMES/Apulcra-genome.fa -V Apul_rnaseq_genotypes-filtered.vcf.gz --exclude-filtered TRUE --select-type-to-include SNP -O Apul_rnaseq_genotypes-filtered-true.vcf.gz
10:37:43.236 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mmfs1/gscratch/srlab/nextflow/bin/miniforge/envs/gatk4/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:37:43.423 INFO  SelectVariants - ------------------------------------------------------------
10:37:43.425 INFO  SelectVariants - The Genome Analysis Toolkit (GATK) v4.6.2.0
10:37:43.425 INFO  SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
10:37:43.425 INFO  SelectVariants - Executing as strigg@n3443 on Linux v4.18.0-513.18.1.el8_9.x86_64 amd64
10:37:43.425 INFO  SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v21.0.7+6-LTS
10:37:43.426 INFO  SelectVariants - Start Date/Time: July 22, 2025, 10:37:43 AM PDT
10:37:43.426 INFO  SelectVariants - ------------------------------------------------------------
10:37:43.426 INFO  SelectVariants - ------------------------------------------------------------
10:37:43.426 INFO  SelectVariants - HTSJDK Version: 4.2.0
10:37:43.426 INFO  SelectVariants - Picard Version: 3.4.0
10:37:43.426 INFO  SelectVariants - Built for Spark Version: 3.5.0
10:37:43.428 INFO  SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:37:43.428 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:37:43.428 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:37:43.428 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:37:43.428 INFO  SelectVariants - Deflater: IntelDeflater
10:37:43.428 INFO  SelectVariants - Inflater: IntelInflater
10:37:43.428 INFO  SelectVariants - GCS max retries/reopens: 20
10:37:43.428 INFO  SelectVariants - Requester pays: disabled
10:37:43.429 INFO  SelectVariants - Initializing engine
10:37:43.613 INFO  FeatureManager - Using codec VCFCodec to read file file:///mmfs1/gscratch/scrubbed/strigg/analyses/20250717_biscuit_Apul/Apul_rnaseq_genotypes-filtered.vcf.gz
10:37:43.652 INFO  SelectVariants - Done initializing engine
10:37:43.751 INFO  ProgressMeter - Starting traversal
10:37:43.751 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
10:37:43.753 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
10:37:43.753 INFO  ProgressMeter - Traversal complete. Processed 0 total variants in 0.0 minutes.
10:37:43.799 INFO  SelectVariants - Shutting down engine
[July 22, 2025, 10:37:43 AM PDT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2076049408