Oktoberfest fails on Sage output with PTMs

[gritukan]

Describe the bug

Hi! When running Oktoberfest over Sage output with PTMs identified crash happens because Sage outputs results not in [UNIMOD:1234] format but just reports PTM masses in [+1234.567] format.

https://pastebin.com/nzhp7Mwy -- stacktrace
https://pastebin.com/3qWArn3X -- config
https://pastebin.com/4zH6xpgc -- first 20 PSMs identified by Sage; some of them have PTMs in the [+1234.567] format

To Reproduce

Any Sage output with PTMs will cause Oktoberfest to crash.

Expected behavior

Oktoberfest does not try to resolve modifications in this format from UNIMOD.

System [please complete the following information]:

Ubuntu 24.04.4 LTS, Python 3.12.3, oktoberfest==0.10.0

[cemilcansaylan]

Hi @gritukan,

Thank you for the nice explanation! When I checked your config file, you specified n-terminal acetylation as var_mod. We are not supporting this modification. Thus, this causes the error when reading the search results. We will add a check in the config for these cases.

Best,