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 GenotypeGVCFs -R /gscratch/srlab/strigg/GENOMES/Pocillopora_meandrina_HIv1.assembly.fasta -V gendb://GenomicsDB -O Ptua_rnaseq_genotypes.vcf.gz
03:47:42.908 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
03:47:43.261 INFO  GenotypeGVCFs - ------------------------------------------------------------
03:47:43.263 INFO  GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.6.2.0
03:47:43.263 INFO  GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
03:47:43.263 INFO  GenotypeGVCFs - Executing as strigg@n3432 on Linux v4.18.0-513.18.1.el8_9.x86_64 amd64
03:47:43.263 INFO  GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v21.0.7+6-LTS
03:47:43.263 INFO  GenotypeGVCFs - Start Date/Time: July 23, 2025, 3:47:42 AM PDT
03:47:43.263 INFO  GenotypeGVCFs - ------------------------------------------------------------
03:47:43.270 INFO  GenotypeGVCFs - ------------------------------------------------------------
03:47:43.270 INFO  GenotypeGVCFs - HTSJDK Version: 4.2.0
03:47:43.270 INFO  GenotypeGVCFs - Picard Version: 3.4.0
03:47:43.270 INFO  GenotypeGVCFs - Built for Spark Version: 3.5.0
03:47:43.272 INFO  GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
03:47:43.272 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
03:47:43.272 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
03:47:43.272 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
03:47:43.272 INFO  GenotypeGVCFs - Deflater: IntelDeflater
03:47:43.272 INFO  GenotypeGVCFs - Inflater: IntelInflater
03:47:43.272 INFO  GenotypeGVCFs - GCS max retries/reopens: 20
03:47:43.273 INFO  GenotypeGVCFs - Requester pays: disabled
03:47:43.273 INFO  GenotypeGVCFs - Initializing engine
03:47:43.278 INFO  GenotypeGVCFs - Shutting down engine
[July 23, 2025, 3:47:43 AM PDT] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2076049408
***********************************************************************

A USER ERROR has occurred: Fasta dict file file:///gscratch/srlab/strigg/GENOMES/Pocillopora_meandrina_HIv1.assembly.dict for reference file:///gscratch/srlab/strigg/GENOMES/Pocillopora_meandrina_HIv1.assembly.fasta does not exist. Please see https://gatk.broadinstitute.org/hc/articles/360035531652-FASTA-Reference-genome-format for help creating it.

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.