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
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).Thank you! Now it is working correctly!
Thanks
If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
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
Log in to answer this question.
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: