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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Can I ask prokka to only produce the gbk file? #430

Closed MolyWang closed 4 years ago

tseemann commented 5 years ago

There is no way to currently disable it except by editing the prokka script and deleting or commenting out the run_cmd("tbl2asn ....."); lines.

tseemann commented 4 years ago

Sorry i mis-read your question. You only want the GBK file? No, but I just run prokka then delete all the files I don't want.

mlbonatelli commented 3 years ago

Hi :) I was wondering if it still not possible to disable the production of the .gbk file through the command line. That would be really convenient for me because I am using prokka on a server. Thanks 😊

andersgs commented 3 years ago

Hi @mlbonatelli. Your question seems to be the opposite of what is asked in this issue.

But, if I understand correctly, the easy thing would be to do something like this:

prokka --outdir tmp contigs.fa && rm -f tmp/*.gbk

That will remove your gbk after it is made...

Is your concern about disk space on the server? Or cpu?

mlbonatelli commented 3 years ago

Hi @andersgs,

You are absolutely right, it is the opposite. I am only writing in this closed issue because @tseemann said something about deleting the line in the script responsible to generate the .gbk file.

The problem is that I am using prokka to annotate a metagenome and it is taking days to finish, and I can see that is because it is generating the .gbk file. Since I am running on a server, I don't have privileges to modify the script, that is why I wondered if I could just use a command on prokka to not produce the .gbk file.

If I just interrupt prokka in this last step, will it somehow compromise the other files?

andersgs commented 3 years ago

I am not that confident that prokka should be used for metagenomic datasets.

But, GBK is the last file produced by prokka and interrupting it won't affect the other output.

The other option is, if your server has conda, is to create your own conda prokka environment. You can then edit the script to comment out the appropriate line.

Best of luck.

andersgs commented 3 years ago

I have not tried it, so have no idea how well it works, but if you have not tried it, it may be worth giving ATLAS a go: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03585-4

mlbonatelli commented 3 years ago

Thanks for the reply @andersgs :) I will check with my collaborators, it was their suggestion to usa prokka to annotate the metagenome. And thanks for the link to ATLAS!