Genome Annotation Output Files Naming

Question

[Fid_o]

I ran this annotation command: for k in *.fasta; do prokka $k --outdir "$k".prokka.output; echo $k; done on hundreds of assembled sequences. Each sequence annotation output produced a folder named "sequence_name.prokka.output" but the actual files in the folders were named according to the date e.g. "PROKKA_03062020.gff" for all the folders.

Now I want the actual output be named with the actual FASTA file ID. Example: sequence ID of D02502 should be like this: "PROKKA_D02502.gff"

What do I add (or remove) from the code above?

Answer 1

[Mensur Dlakic]

for k in *.fasta; do prokka $k --outdir "$k".prokka.output --prefix PROKKA_$k; echo $k; done

[Fid_o]

Thank you sooooo much Mensur Dlakic.

I am learning Bioinformatics and your help is great.

[Ahmed Ezat El Zowalaty]

Is there a way to put all prokka output from all fasta files in one folder rather than the traditional output (one folder for the output of each fasta)?