Hi,
I think I have a related error (if not, I'm sorry, I'll start a new thread). I have followed the directions on the Trinotate installation website for installing rnammer. I've changed the $HMMSEARCH_BINARY and $INSTALL_PATH to the correct paths, I've installed hmmer2.3, and I've removed --cpu 1 from the core-rnammer script in both places, but although rnammer doesn't give any errors, it doesn't quite seem to be running correctly. When running the example command, it doesn't create new ecoli.fsa, ecoli.gff, or ecoli.hmmreport files, instead, it creates these:
temp.21166.fsa
Any ideas about what is happening?
Thanks for your help,
Karen