Welcome @angelo_chan
I think we can help!
There is a new known issue with the job container configuration for some versions of the fixmate tool. This was tracked about a month ago and the correction is still pending.
- Details at → Configuration issue snippy 4.6.0+galaxy0 && 4.5.0 · Issue #1415 · galaxyproject/usegalaxy-tools · GitHub
I’m curious if that same step being called independently is also a problem (this would be the first report!). I would like to review closer. Would you be able to share the version you are running, and confirm the server is UseGalaxy.org.au? Find the version at the very top of the tool form.
You could also try a test: toggle into and use an earlier tool version. One back is usually enough when there are small configuration issue with the initial deployment across some of the larger instances (a new Galaxy release came out earlier this week, and learning about small things is great so we can squash the problem! ).
Other than this, I would generally suggest filtering a BAM before using this tool. Some minimum mapQ, primary alignments, proper pairs, and especially removing unmapped! Those records would usually be discarded anyway, and will help this tool to process larger primary data.
Finally, as an extra note, I can let you know that any BAM dataset with the datatype bam is coordinate sorted. This tool is intended to be run as part of a workflow that can consume any BAM and not fail for a technical reason, so the developer decided to bundle the two actions (required queryname sorting followed by fixmate). Not ideal for all use cases! But if the operation failed with one tool, it would fail with any others that called it in a bundle, which is why I think there is something else special going on and would like to review.
More details about BAM data are in this topic if curious!
We hope this helps, and please let us know if you are able to get this to run with a different version! 