Hi,

I'm currently looking to train Augustus using optimize_augustus.pl, on a set of 1000 genes with UTRs in genbank format. I'm slightly confused by the instructions given here:

http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=Augustus.UTRTraining

where the command is:

optimize_augustus.pl --species=yourSpecies --cpus=8 --rounds=3 bothutr.gb.train --UTR=on --metapars=/pathToYourAUGUSTUS/config/species/yourSpecies/yourSpecies_metapars.utr.cfg --trainOnlyUtr=1

I think the above is for training UTR parameters when normal parameters for the species of interest already exist. Does anyone have any experience training both normal (CDS) and UTR parameters from scratch? Should I first train the normal parameters and then the UTR parameters with two separate runs of optimize_augustus.pl, or is it possible to do both at the same time?

This is my current command (which I hope is doing both simultaneously, I have removed --metapars and --trainOnlyUtr):

optimize_augustus.pl --species=myspecies --cpus=6 1000genes.gb --UTR=on

Cheers, Rory