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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Use eggnog to annotate #353

Closed HENdavid closed 5 years ago

HENdavid commented 5 years ago

Dear Torsten,

I been using prokka for many years as a base for annotation and comparative genomics together with roary, now I have some issues. I am using version 1.13 (brew) and I got no CRISPR annotation for my genomes, I know it is being fixed in version 1.14, any idea when it is gonna be available the update? Also for annotation, I found I bit disappointing when annotate my genomes with the standard databases that comes ready with prokka, I would like to use EGGNOG 4.5/5 (HMM) database instead, any chance to implement this in the last update or it is possible to covert it as a custom database, if so can you guide me a little bit.

Thanks in advance, I really enjoy using prokka!

harish0201 commented 5 years ago

IIRC, for eggNOG or any custom hmms you need to press the new custom hmm files and add it to the db/hmm folder in the prokka directory. There should be no need to modify the script as I believe it was fixed in the commit below.

I was able to find this: https://github.com/tseemann/prokka/commit/31efd38ae8322d03614c1f727cb5b65f15b7c4ee

The CRISPR information should be present as product=CRISPR-associated in the gff files.

tseemann commented 5 years ago

@HENdavid thank you to @harish0201 for helping here. You need to get HMMER 3.x formatted database files for the eggNOG database, and then just provide them via the --hmms option.