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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Prokka stops without generating files and without offering an apparent error #530

Open LRT-14 opened 3 years ago

LRT-14 commented 3 years ago

This is the command I use:

prokka --compliant --centre X --locustag M --outdir XXX --force --prefix XX --addgenes --genus Lactiplantibacillus --species plantarum --strain XXX --rfam --setupdb Bacteria --cpu 4 --kingdom Bacteria --gcode 11 contigs.fasta

It runs for 2 seconds, and then stops like this:

[12:52:25] Looking for databases in: /var/lib/prokka/db [12:52:25] Kingdoms: [12:52:25] Genera: Enterococcus Escherichia Staphylococcus [12:52:25] HMMs: [12:52:25] CMs: Archaea Bacteria Viruses

And no files appear in the folder XXX ¿what I am doing wrong? Any help? Thank you.

kapsakcj commented 3 years ago

It could be looking for a Lactiplantibacillus genus database, which doesn't exist unless you are using your own database. Try removing that option and re-running.

Also, the --genus flag is no longer recommended https://github.com/tseemann/prokka#the-genus-databases.

On another note, the --setupdb flag should only be run once after installing prokka, to index the provided databases. You should also remove that flag from your command as well.

LRT-14 commented 3 years ago

So, do I have to remove the options --strain and --species as well? and then add the option --proteins? If I do so, in which databases exactly does it search to assign function?

LRT-14 commented 3 years ago

I have just use this command:

prokka --compliant --centre XXX --locustag M --outdir prokka --proteins --rfam --cpus 4 --kingdom Bacteria --gcode 11 final_contigs2.fasta

Now, it finishes and files are generated in the output directory, but I see that no rRNA is annotated, this is weird...

kapsakcj commented 3 years ago

I believe both --strain and --species are options for simply labeling so it shouldn't matter if you use them or not. I don't believe they affect any of the annotation steps.

I would check the output/log to see if there is any clues as to why no rRNA was annotated. I would first ensure that the tools/dependencies for rRNA are installed & functioning, and then investigate other reasons if they are indeed installed

LRT-14 commented 3 years ago

Thank you for your comments once again. I noticed that barrnap what not appropiately installed. Now it works.

Additionally, I want to ask you about what the flag --proteins exactly does, the results using it or not were different:

The rest of items were the same in both ways.