Annotations did not match contig names about pirate HOT 3 CLOSED

Hi Noah,

I am surprised. If you have annotated using prokka on default(ish) settings there shouldn't be any issues. That warning appears if the first field in the GFF3 annotation lines does not match the names of the contigs at the bottom of the file. Which version are you using? Could you send me a few example files for me to test? I have just pushed a new version and it maybe a bug I have introduced.

All the best,
Sion

from pirate.

Hi Sion,
I just sent you an email containing the files that caused the error. They were annotated using prokka version 1.14.6 and I attempted to run PIRATE version 1.0.3.
Best,
Noah

from pirate.

Hi Noah,

Having looked at the files there is an obvious discrepancy between annotation and fasta headers for contig '0'. In the prokka GFFs contig 0 has been renamed to SEQ in the annotation line (col 1). This is most likely due to the your contig naming scheme having 0 as a fasta header which maybe interpreted as binary 0 (empty) by some programs in prokka.

In short, this isn't a PIRATE issue but one caused by the input being non-standard. If you rename the contig headers starting from 1 and reannotate them you shouldn't have an issue.

All the best,
Sion

from pirate.