bakta encounters issues annotating assemblies with presence of N's

[plaquette]

hey, i have some assemblies that i want to annotate.

it works fine when

• i annotate using prokka
• remove the N's by hand

but fails with ERROR: genome file (test.fa) not valid! when there are N's in the sequences.

i use bakta v1.7.0 installed via conda and call it like this:

bakta --db db-light --verbose --output test --locus test --locus-tag test --threads 10 --skip-plot --strain test --complete test.fa

one example is attached (now with .txt extension instead of .fa - i was not allowed to upload it with the original extension):
test.txt

concluding from this issue #87 it should work with the N's
... what can i do to fix this?

Thank you very much!

Best,

j.

[oschwengers]

Hi @plaquette,
thanks for reporting. Unfortunately, I cannot reproduce this issue. I tested your file with Bakta v1.8.1 and v1.7.0, and both worked just fine. There was once an issue with - within sequences (#87) but this is not related to Ns, they should work just fine.

This leaves me a bit puzzled. Could you execute Bakta in --debug mode and provide the logs?

[plaquette]

hey @oschwengers - sorry for the very delayed answer, i was on vacation.

it seems, that i can not reproduce my errors from last month...

therefore the issue can be closed. sorry for bothering you & thank you.

best,

p.