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 VariantFiltration -R /gscratch/srlab/strigg/GENOMES/Apulcra-genome.fa -V Apul_rnaseq_genotypes.vcf.gz -O Apul_rnaseq_genotypes-filtered.vcf.gz --filter-name FS --filter FS > 60.0 --filter-name QD --filter QD < 2.0 --filter-name QUAL30 --filter QUAL < 30.0 --filter-name SOR3 --filter SOR > 3.0 --filter-name DP15 --filter DP < 15 --filter-name DP150 --filter DP > 150 --filter-name AF30 --filter AF < 0.30
10:37:39.390 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
10:37:40.089 INFO  VariantFiltration - ------------------------------------------------------------
10:37:40.092 INFO  VariantFiltration - The Genome Analysis Toolkit (GATK) v4.6.2.0
10:37:40.092 INFO  VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/
10:37:40.092 INFO  VariantFiltration - Executing as strigg@n3443 on Linux v4.18.0-513.18.1.el8_9.x86_64 amd64
10:37:40.092 INFO  VariantFiltration - Java runtime: OpenJDK 64-Bit Server VM v21.0.7+6-LTS
10:37:40.093 INFO  VariantFiltration - Start Date/Time: July 22, 2025, 10:37:39 AM PDT
10:37:40.093 INFO  VariantFiltration - ------------------------------------------------------------
10:37:40.093 INFO  VariantFiltration - ------------------------------------------------------------
10:37:40.093 INFO  VariantFiltration - HTSJDK Version: 4.2.0
10:37:40.093 INFO  VariantFiltration - Picard Version: 3.4.0
10:37:40.093 INFO  VariantFiltration - Built for Spark Version: 3.5.0
10:37:40.095 INFO  VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:37:40.095 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:37:40.095 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:37:40.095 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:37:40.095 INFO  VariantFiltration - Deflater: IntelDeflater
10:37:40.095 INFO  VariantFiltration - Inflater: IntelInflater
10:37:40.095 INFO  VariantFiltration - GCS max retries/reopens: 20
10:37:40.095 INFO  VariantFiltration - Requester pays: disabled
10:37:40.096 INFO  VariantFiltration - Initializing engine
10:37:40.296 INFO  FeatureManager - Using codec VCFCodec to read file file:///mmfs1/gscratch/scrubbed/strigg/analyses/20250717_biscuit_Apul/Apul_rnaseq_genotypes.vcf.gz
10:37:40.341 INFO  VariantFiltration - Done initializing engine
10:37:40.462 INFO  ProgressMeter - Starting traversal
10:37:40.463 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
10:37:40.465 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
10:37:40.465 INFO  ProgressMeter - Traversal complete. Processed 0 total variants in 0.0 minutes.
10:37:40.488 INFO  VariantFiltration - Shutting down engine
[July 22, 2025, 10:37:40 AM PDT] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2076049408