avonm

What does your .faa file look like? I don't know which format the header should be in for prokka to actually annotate the CDS accoridng to my .faa file.

@mikeyweigand I did get it to work but now I have switched to bakta. The header in the proteins file look like this: >ABV20485.1 2.7.2.4~~~thrA~~~aspartokinase/homoserine dehydrogenase I >AY513487.1 ~~~cosD~~~PCFO71 CosD...