Error running Prokka

Question

[bioaitana26]

Download and installed the latest version of prokka and I checked with prokka. Then printed the help screen with all available options.

after make a new directory for the annotation:

cd ~/
mkdir annotation
cd annotation

Link the metagenome assembly file into this directory:

ln -fs ~/home/genome.fa

and after

prokka genome.fa --outdir prokka_annotationPr8x  --cpus 2

but I had this error. What happen? my genome.fa is not good?

[11:37:57] This is prokka 1.12
[11:37:57] Written by Torsten Seemann <[e-mail]>
[11:37:57] Homepage is https://github.com/tseemann/prokka
[11:37:57] Local time is Mon Jun  3 11:37:57 2019
[11:37:57] Operating system is linux
[11:37:57] You have BioPerl 1.007002
[11:37:57] System has 2 cores.
[11:37:57] Will use maximum of 2 cores.
[11:37:57] Annotating as >>> Bacteria <<<
[11:37:57] 'genome.fa' is not a readable non-empty FASTA file

thank you very much

[lieven.sterck]

hi bioaitana26,

I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

Answer 1

[AK]

Hi bioaitana26,

Can you try checking ls -l ~/home/genome.fa, or the content of your soft link, or using ~/home/genome.fa directly without creating a soft link? In the script, it tests for -r, -d (not), and -s:

my $in = shift @ARGV or err("Please supply a contig FASTA file on the command line.");
(-r $in and !-d _ and -s _) or err("'$in' is not a readable non-empty FASTA file");

Where:

• -r File is readable by effective uid/gid;
• -d File is a directory;
• -s File has nonzero size (returns size in bytes).

Answer 2

[Joe]

I think you need to check that genome.fa is what you think it is, as that workflow, works for me (I'm using prokka 1.11, but I doubt that'll make a difference).

Answer 3

[bioaitana26]

Thank you! Now it is working correctly!

Thanks

[lieven.sterck]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

[nisrinalulu]

Dear Bioainata26,

I have same problem with you. How do you solved your problem? Do you run script like SMK mentioned?

Thank you for your help,

Regards,

Lulu