Oliver Schwengers

Hi Dany, thanks for reaching out. Yes, DB size is sometimes and for some users an issue. As we decided to come up with a taxonomically untargeted approach and database,...

Hi Håkon, thanks for reaching out and reporting. This is indeed a wrong functional annotation. Unfortunately, this is due to a false annotation in the related UniProt UniRef100 und UniRef90...

Hi @hkaspersen , FYI, I just released version [v1.5.0](https://github.com/oschwengers/bakta/releases/tag/v1.5.0) introducing an improved pre-annotation of the PSC based on NCBIfams. A first quick test showed that in your case (above) the...

`MobileElementFinder` is also an interesting option: - https://doi.org/10.1093/jac/dkaa390 - https://cge.cbs.dtu.dk/services/MobileElementFinder

Hi @alexweisberg , thanks a lot for reaching out with these thorough considerations. We've thought about this a lot and I'd love to enhance annotations of T?SS -and MGE-related proteins...

Hi, thanks for reaching out with this. That's interesting! Could you maybe provide the log file of a verbose run (`bakta --verbose ...`) and maybe also a debugging file triggering...

Thanks! This is indeed due to BioPython and I guess it relates to a recent deprecation of the `Bio.Alphabet` module within BioPython: https://github.com/biopython/biopython/issues/3156 Actually, conda should take care that the...

Indeed, the causing line 631 of `Bio/SeqIO/InsdcIO.py` occurs in BioPython `1.74`: https://github.com/biopython/biopython/blob/8677e94d3d4ca7374e12d66a05e0dd3732168cce/Bio/SeqIO/InsdcIO.py#L631 Could therefore please update BioPython to `1.78` or `1.79` and try again?

@kitka2000 , *gentle ping* Did this solve the issue?

Oh, indeed I've somehow overseen your msg, my fault - sorry! These version conflicts often happen within overcrowded environments where several tools require different versions of the same 3rd party...