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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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commande line #703

Open azouradel opened 4 months ago

azouradel commented 4 months ago

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

marco315176 commented 2 months ago

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