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
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 <firstname.lastname@example.org> [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