I actually was able to solve this for myself. As often happens, I went to ask for help on Slack but first wanted to understand the problem better. Turns out, our old IT director (who was not loved in the dept because he was constantly taking away permissions) decided to make life 'easy' for us by creating a bash script that created the sbatch file for us. Debugging this file showed that it did not work correctly when using local installs. I was able to simply write my own sbatch file.
I submitted the fix to the IT team but I don't even know if anyone has the permissions to get in and fix it right now.
I submitted the fix to the IT team but I don't even know if anyone has the permissions to get in and fix it right now.