I’m encountering a persistent issue while running a Galaxy workflow on Jetstream2. One of the steps fails with the following error:
/jetstream2/scratch/main/jobs/69270630/tool_script.sh: line 23: /dev/null: Permission denied
This occurred during the execution of the NCBI Foreign Contamination Screen (FCS) workflow at step 2 (NCBI FCS GX). The job ID is 69270630.
It seems that the job environment does not have appropriate access to /dev/null, which is likely causing the failure. Based on similar cases, this could be due to a misconfiguration in the container, compute node, or scratch filesystem.
Could you please investigate and advise whether this is a node-level or environment-level issue? I’d be happy to provide additional logs or access details if needed.
This tool has a few revisions to keep up with changes at NCBI. Using the most current would be strongly recommended. With so many Galaxy servers and so many tools, all under constant revision and with custom settings, you might need to update tools that are included in workflows on specific servers to match what that server hosts.
Now, this tool might be failing anywhere, any container. I’ll double check and work with the GTN to update as needed.
What to do
If you are working at UseGalaxy.org (where I was testing) the most current version is Galaxy Version 0.5.5+galaxy1 for three of the tools included, and the adaptor tool didn’t change and is still at Galaxy Version 0.5.0+galaxy0.
I was able to simply update the tool version in the GTN workflow, save, and run without any complicated changes to the parameters. This works about the same as the tool form directly. Open the workflow in the editor, click on the tool, modify the version(s), double check parameters are OK (new params, defaults), save, and run.
