Hi,
I am running PROKKA for the very first time and ran a test on a bacteria (NOT E.coli).
I ran this cmd, expecting to get a gene with gene name:
prokka --outdir assembly_test/mydir_genes --prefix mygenome --addgenes assembly_test/assembly.fasta
What I get is this [no gene name, mostly]:
>BFMIPPFK_00026 Lipid A biosynthesis myristoyltransferase
I thought maybe I need to set up a specific db for the bacteria I am using - But I couldn't find how to do it in the manual. I saw this cmd - but I was not clear on what files this needs to run.
--setupdb Index all installed databases
I also saw an option to add --species but it didn't change anything when I ran it (I might have not used it right - I just wrote the name of my baceria)
Any help would be appreciated,
I have also downloaded the Genbank of a reference genome and ran it using --proteins. It gives similar results...
The Genbank looks like this:
The resulting names are the product not the gene name...
I also tried using the --addgenes flag with the exact same results:
I have checked the CSV file and this contains the right gene name. I assumed the "--addgenes" flag didn't work so tried it again with --compliant and --rawproduct
Could it be a problem with the order of flags? I went over the manual several times - if the answer is there I was not able to find it...
Did you check the GenBank output (.gbff, if I am not mistaken), or the .gff output? What names are added to these files?
I can see the gene names I was expecting in the GFF file generated - as well as the CSV, just not the final fnn/faa files :(