I am using RNAmmer version 1.2, available after sign-up at http://www.cbs.dtu.dk/services/RNAmmer/, for download from an e-mailed link. I've followed updated instructions at https://blog.karinlag.no/category/rnammer/ and www.cbs.dtu.dk/services/RNAmmer/instructions.php As such I do not observe any run errors.
In the RNAmmer paper at https://www.ncbi.nlm.nih.gov/pubmed/17452365, it says that for eukaryotes (which fungi are), 5.8S is not yet predictable, but the remaining LSU components - 5S, and 28S can be predicted, and so can the 18S SSU.
What I am confused about is that RNAmmer ver1.2 returns predictions for an "8S_rRNA" subunit. But I cannot find anything about an "8S_rRNA" subunit. Am I mistaken?
I was suspicious this RNAmmer ver1.2 may predict 5.8S_rRNA, not possible with ver1 (?), and this 8S_rRNA is a systematic typo error. So, I searched an example sequence prediction at NCBI BLAST against nr database, but it only yielded a pretty good match to a fungal "5S ribosomal RNA rRNA" - Score = 209 bits (113), Expect = 9e-5, Identities = 115/116 (99%), Gaps = 0/116 (0%).
So back to square one - I've contacted the authors Peter Fischer Hallin and Karin Lagesen about this observation. Since RNAmmer is not really supported formally, I am not hopeful of a prompt reply. Could someone on this forum please throw light on my problem, and help clear my confusion? Thanks!