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Issue
I installed bakta v1.8.2 via conda, the installation was successful but bakta was not operational (it fails and provides an error message - see below). I compared that environment with an older environment (same bakta version) that runs fine and realized that it might be related to some dependencies.
Solution
After a few trials and errors, I downgraded diamond from v2.1.9 to v2.1.8 and ncbi-amrfinderplus from v3.12.8 to v3.11.26 and could successfully use bakta v1.8.2. I did not check all versions in between for ncbi-amrfinderplus.
Note
The error was reproduced with different input files - file content does not appear to matter much.
The problem seems to also extend the latest version (v1.9.3 as of last week), although I did not fully test that version (and therefore did not identify which downgrades were required).
The text was updated successfully, but these errors were encountered:
Hi and thanks for reporting both issues and potential solutions!
There is an issue with Diamond in v2.1.9 and downgrading to v2.1.8should do the trick until there is an upstream patch for Diamond.
Regarding AMRFinderplus: They recently updated its database scheme. Best you can do is to update both AMRFinderplus and its database as @mmcguffi suggested.
@mmcguffi Is there a specific issue with BioPython? If so, could you please open a dedicated issue for that? I wasn't aware of that.
Issue
I installed bakta v1.8.2 via conda, the installation was successful but bakta was not operational (it fails and provides an error message - see below). I compared that environment with an older environment (same bakta version) that runs fine and realized that it might be related to some dependencies.
Command, log and error message
Solution
After a few trials and errors, I downgraded diamond from v2.1.9 to v2.1.8 and ncbi-amrfinderplus from v3.12.8 to v3.11.26 and could successfully use bakta v1.8.2. I did not check all versions in between for ncbi-amrfinderplus.
Note
The error was reproduced with different input files - file content does not appear to matter much.
The problem seems to also extend the latest version (v1.9.3 as of last week), although I did not fully test that version (and therefore did not identify which downgrades were required).
The text was updated successfully, but these errors were encountered: