prokka --setupdb issue

Question

[littlemicrobiologist]

I wish to do gene annotation using prokka on my linux environment. but I am getting the following thing only instead of answer. I don't know where I made mistake.

The command I used:

prokka --outdir /home/prokkareport /home/annotation/finalized_contig_fasta

The result:

[20:43:37] This is prokka 1.14.5
[20:43:37] Written by Torsten Seemann <[e-mail]>
[20:43:37] Homepage is https://github.com/tseemann/prokka
[20:43:37] Local time is Tue Feb 14 20:43:37 2023
[20:43:37] You are .........
[20:43:37] Operating system is linux
[20:43:37] You have BioPerl 1.7.7
Argument "1.7.7" isn't numeric in numeric lt (<) at /usr/bin/prokka line 259.
[20:43:37] System has 16 cores.
[20:43:37] Will use maximum of 8 cores.
[20:43:37] Annotating as >>> Bacteria <<<
[20:43:37] The sequence databases have not been indexed. Please run 'prokka --setupdb' first.

Then I ran prokka --setupdb but it is not working

Answer 1

[Mensur Dlakic]

It helps to run prokka -h as that will give you some useful information. It also helps to read through the prokka description on GitHub.

If you simply run prokka --setupdb, the program will try to guess the location of databases. It is usually in /where/prokka/is/db such that first 3 subdirectories are replaced by actual directory where prokka resides. It may help to explicitly say where the databases are. If they are not in the expected directory, please don't ask me where they are because you installed the program. So:

prokka --setupdb --dbdir /where/prokka/is/db

prokka --listdb will tell you what databases are installed and recognized by the program. If the output of that command is empty, it means that databases are not set up properly. Plenty on information about all of this on prokka GitHub site.