Hi all, I ran into a pretty serious bug with the

merge_taxonomy.py

script that I saw was posted to the issue tracker in 2025 (this was using the latest 4.0.0 release). The issue is marked as ‘requires-upstream-fix’ but seems to be dormant with no response. I could post a possible fix for this (at the moment it’s centered on AMR), but I wanted to know if there was any reason this was marked as upstream. Thanks!

Hi @Chris Fields thanks for the report and sorry for the long unfixed bug 😞, and I just the additional comments on the issue. Unfortunately both Jasmin and I have changed jobs almost at the same time (we have an announcement coming) so we are both having to shift into minimal maintenance mode... Anan also left quite a while ago (the main developer of AMPCombi) too... But this does mean we are looking for new developers/helpers to keep the pipeline itself going. Givne it looks like you're already lookniug into the code (plus with a little 🤖 friend), is this somehting you would consider helping out with (either on regular or small basis?)

I could help out with pull requests and other fixes, there are some areas like this, taxprofiler, bacass, mag, etc that I could assist. I’m a bit wary of committing too much time since I’m the full-time director of a core facility, but there are definitely areas I could help with since we deal quite a bit with microbiome and metagenome data

That would be much appreciated, completely understand the context!