The sequence databases have not been indexed. Please run 'prokka --setupdb' first.

Question

[JAB]

Dear Friends,

I am trying to annotate an assembled genome using prokka

prokka MULTIFASTA.fa  --usegenus --genus vibrio --species parahaemolyticus  --outdir VP81_ANNOTATED --prefix VP81

When running the above command I get this error below:

[02:21:09] This is prokka 1.14.5
[02:21:09] Written by Torsten Seemann  <[e-mail]> 
[02:21:09] Homepage is> https://github.com/tseemann/prokka
[02:21:09] Local time is Tue Oct  27 > 02:21:09 2020 
[02:21:09] You are root 
[02:21:09] Operating system is linux 
[02:21:09] You have BioPerl 1.7.7
**Argument "1.7.7" isn`t numeric in numeric lt (<) at usr/bin/prokka line 259**
[02:21:09] System has 4 cores. 
[02:21:09] Option --cpu asked for 8 cores, but your system only has 4
[02:21:09] Will use maximum of 4 cores. 
[02:21:09] Annotating> as >>> Bacteria <<<
 [02:21:09] The sequence databases have not been indexed. Please run 'prokka --setupdb' first.

---

I tried to solve it typing prokka --setupdb but anything changes.

Could you give any advice?

Thanks in advance!

[JAB]

Dear Mensur,

Unfortunately I tried it scripting

prokka --usegenus --genus vibrio --species parahaemolyticus --outdir VP81_ANNOTATED --prefix VP81 MULTIFASTA.fasta

However it didn't work.

I think it is possible that the trouble comes from the installation of Bioperl :

Argument "1.7.7" isn`t numeric in numeric lt (<) at usr/bin/prokka line 259

Or with the indexed sequence databases, for examples after run prokka --setupdb I got:

Looking for database in:/var/lib/prokka/db *Kingdoms: *Genera: Enterococcus Escherichia Staphylococcus * HMMs: *CMs: Archea Bacteria Viruses

Thanks in advance, JAB

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

[Mensur Dlakic]

It would have been helpful if you gave the full error message from the beginning. It seems this is a problem for prokka team, which is easy to find by googling that error message:

https://github.com/tseemann/prokka/issues/508

[JAB]

Thak you so much, I spent a lot of time looking for an explantion.

Answer 1

[Mensur Dlakic]

File name (MULTIFASTA.fa) comes as the last argument on the command line.