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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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HMM not indexed #640

Open btredcup opened 2 years ago

btredcup commented 2 years ago

I use prokka a lot but having an issue with my HMM file. I am using a custom database and used hmpress prior running to index the HMM file. However, I am getting this error: Your HMM is not indexed, please run: hmmpress miniconda3/envs/perl/db/hmms/all_phrogs.hmm

I am running ~14,000 phage genomes as a combined fa file. When I run an individual genome through, it doesn't have any issues with the HMM file

Any insight would be greatly appreciated. Thanks

MichaelAngelou commented 1 year ago

hello @btredcup @tseemann May I ask if your able to solved this error? To put simply, I downloaded the prebuilt PHROGS hmm database from Millards lab, and copied it to the /home/dostvip2/miniconda3/db/hmm directory as suggested. However, I'm getting the same error in using the phrogs database even after running the prokka --setupdb.

Prokka seems to recognize the database though. (base) dostvip2@DESKTOP-L5H6T8M:/mnt/f$ prokka --listdb [09:40:27] Looking for databases in: /home/dostvip2/miniconda3/db [09:40:27] Kingdoms: Archaea Bacteria Mitochondria Viruses [09:40:27] Genera: Enterococcus Escherichia Staphylococcus [09:40:27] HMMs: all_phrogs HAMAP pvogs2020 [09:40:27] CMs: Archaea Bacteria Viruses

Thank you very much.