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Error running Prokka
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15 months ago

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 <torsten.seemann@gmail.com>
[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

software error • 218 views
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hi bioaitana26,

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16 months ago
SMK ♦ 1.3k
Ghent, Belgium

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).
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7 months ago
Joe 12k
United Kingdom

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).

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15 months ago

Thank you! Now it is working correctly!

Thanks

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