Invalid or corrupt jarfile error
Answered
I'm trying to use GATK version 4.3.0.0, but I've started getting an invalid or corrupt jarfile error for any command I use other than `gatk --help`. For example:
gatk --version
Using GATK jar /wynton/home/lo/bensinger/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar
Running:
/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-4.3.0.0/gatk-package-4.3.0.0-local.jar --version
Error: Invalid or corrupt jarfile /wynton/home/lo/bensinger/gatk-4.3.0.0/gatk-package-4.3.0.0-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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Hi Benjamin Singer,
Thanks for writing into the forum with this issue! Most likely there was something wrong when you tried to install gatk. We don't maintain conda or bioconda so I can't determine if that solution would work. But downloading directly from GATK, I recommend following these instructions: https://github.com/broadinstitute/gatk#downloading-gatk4.
If you try that and it still doesn't work, we can look into other possible issues.
Best,
Genevieve
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Hi Benjamin Singer,
It has been a while since we've heard from you, so we'll be closing out this ticket in our system. However, please note that if you still require assistance, you need only respond to this thread, and we can swiftly re-open your ticket and pick up where we left off.
Thank you for being a valued contributor to the GATK community!
Best,
Genevieve
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