inconsistency in prokka annotation

[vappiah]

Hi @tseemann I observed an inconsistency when annotating a genome with prokka.

First I downloaded the M. ulcerans Agy99 genome ( fasta and genebank format).

I performed annotation on the fasta file specifying the genebank as proteins with the command below.
prokka --cpus $threads --kingdom Bacteria --prefix Agy99 --genus Mycobacterium --rfam --species ulcerans --cdsrnaolap --metagenome --proteins Agy99.gb Agy99.fasta

I counted the CDS in the original genebank file and that of the prokka generated genebank. The original had 4160 whiles the prokka file had 8665. Am i missing something in the command ? I was expecting similar values for both but the difference is very large. Please advice. Thanks

[felipelira]

Dear vappiah,

Did you check if this difference between numbers means that your new annotation presents pseudo genes or fragmented genes?

Cheers

[vappiah]

Dear @felipelira They are fragmented genes.

[felipelira]

In this manner, how many genes you get when filtering the fragmented genes? Is it close to the expected 4160 genes? Another question. Why do you use the option "metagenome"?