Can anyone advise how long RnammerTranscriptome.pl (the final annotation step of Trinnotate, prior to assembling the sql database) typically takes to run on a eukaryotic transcriptome ~ 55 k contigs? I am running this on an HPC for the past 24 h and although I haven't received any errors, and things seem to be running OK, there have been no files produced after .fsa and .lsu.cf for the past 20 h. Is this normal?

Your experiences with this are welcomed.