CODEWITHSUNDEEP
condahpcgatk
agre945
agre945

Reputation: 1

GATK jar file not found- Using GATK on an HPC

I am working on jupyter nesi for my project, and previously set up my own personal conda environment (last year ) using the guidelines specified here (https://support.nesi.org.nz/hc/en-gb/articles/360001580415-Miniconda3). (My conda environment = /home/agre945/.conda/envs/miss-molly

I used conda (via the terminal and my notebook set to my conda environment) to download gatk: (conda install bioconda/label/cf201901::gatk4 - https://anaconda.org/bioconda/gatk4), which was working fine.

Now, when I run which gatk I can see it's in my environment bin, but when I run 'gatk version' or try to run any script that uses gatk I get the error 'invalid or corrupt jarfile'.

I tried downloading the package from gatk and unzipping it on nesi, but got the same error. I also tried downloading an older version from an archive and using 'gatk -register'as suggested here : https://github.com/faircloth-lab/phyluce/issues/112, but still got the same error message.

I have tried reinstalling via conda, but the .jar file is always invalid. I am unsure if this is to do with my conda environment? Any help would be great.

Upvotes: 0

Views: 119

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