Unusually high ncRNA detected on same contig & coordinate - Archea

[naturepoker]

Hi,

Before I begin, thanks for the wonderful pipeline! Without Prokka I wouldn't be able to study half the things I'm doing right now.

Prokka annotation of our lab's Haloarchaeal genome seems to be picking up about 3x to 4x the number of ncRNA seen in other members of the particular genus, and I was wondering if there are some quirks I should be aware of when annotating an Archael genome with Prokka (with specific goal of looking for ncRNA).

It looks like the genome contains about 130 ncRNA hits (against ~30 to ~40 of genomes of comparable species) and the vast majority of them seem to occur on the same 1..30 coordinate of the chromosomal contig.

For example, I'm guessing "61 ncRNA 61 contig1 1..30" on the log file implies 61st ncRNA on contig 1, from bases 1 to 30. I'm getting about a hundred of the same hits referring to contig1 1..30.

What do you think? Is Prokka picking up multiple similar hits (rfam I guess?) from the same 1-30 bp region in this case? Am I looking at a strange bug?

Thank you!