Open Daniel-Tichy opened 1 week ago
Hi, thanks for reaching out. To make sure that I correctly understand what you're finally trying to achieve: you would like to annotate a phage genome sequence with Bakta using a user-provided proteins file with functional annotations from Phanotate? Is this correct?
The issue is related to the user-provided proteins feature and its associated issues.
I am trying to use bakta to perform annotation on a phage predicted protein file that used Phanotate. I was expecting an annotation to every protein of my input file but it seems that overlapped proteins are being filtered by bakta.
-I would like to deactivate the overlap detection so bakta does not filter the previously predicted proteins that I am using as input.
Example: this is my input gbk for bakta.
I parse it and input it in the following format to bakta.
But I get this output, the protein for WARQSXNU_10 is missing probably because of the overlap in the genome.
I am currently running bakta with this line within a docker.
bakta --db $bakta_db/ --protein $faa_input_bakta --skip-trna --skip-tmrna --skip-rrna --skip-ncrna --skip-ncrna-region --skip-crispr --skip-pseudo --skip-gap --skip-ori --skip-plot --output ${assembly_input_bakta.simpleName}_bakta/ --threads ${params.threads} $assembly_input_bakta