I have a draft genome of a teleoist fish, which is comprised of ~20k scaffolds in a single multifasta file. I intend to run GlimmerHMM for this multifasta file using zebrafish (related species) pretrained set. But after run complete, it only output gff annotation for the first scaffold in multifasta file. How can I obtain GlimmerHMM output for all scaffold? (I have considered the option of spliting this multifasta file and run GlimmerHMM one by one by looping command, but is there any other better solutions?)
Thank you very much in advance for your suggestion! Best regards.