commande line

[azouradel]

I'm trying to use this command line to annotate several genomes in FASTA format that exist in a directory, but the problem is that it only annotates one genome

command line: prokka allgenomes/*.fna --prefix prokka

[Marcopterix]

You could try:

for assembly in /home/PATH/to/*.fna; do
ID=$(basename ${assembly} | cut -d '-' -f '1') #Or wherever your sequence ID is
ename=$(basename ${assembly} | cut -d '.' -f '1')

prokka ${assembly} --kingdom x --outdir /home/PATH/TO/YOUR/OUTDIR/prokka/${ID}_anotated