I'm trying to use GATK version 188.8.131.52, but I've started getting an invalid or corrupt jarfile error for any command I use other than `gatk --help`. For example:
Using GATK jar /wynton/home/lo/bensinger/gatk-184.108.40.206/gatk-package-220.127.116.11-local.jar
/wynton/home/lo/bensinger/miniconda3/bin/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 /wynton/home/lo/bensinger/gatk-18.104.22.168/gatk-package-22.214.171.124-local.jar --version
Error: Invalid or corrupt jarfile /wynton/home/lo/bensinger/gatk-126.96.36.199/gatk-package-188.8.131.52-local.jar
My Java version is OpenJDK 1.8.0_152-release. My Python version is Python 3.9.12.
I've looked up several older posts on this error message and tried to implement their solutions. I tried rerunning `
conda install -c bioconda gatk`, but this didn't change any of the behaviors. I changed the GATK script to include a full filepath to my Java version, but that didn't change anything. The only other thing that has apparently worked is rebuilding Ubuntu from scratch. I'm on a shared HPC cluster so this is not an option for me. Any advice would be very much appreciated.
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