augustus hints and "No feasible path found in HMM" error message
Posted: Thu Nov 19, 2015 7:55 pm
Originally posted in the old forum by Rajat S. Roy on 15.11.2012 - 20:28
I was using augustus with some hints and I keep getting "No feasible path found in HMM"error message for many combination of these hints. It seems like the HMM mechanism is overfitting the hints and some transition/ emission probabilities might be going to zero. Is there a quick way of fixing this?
I was using the following command:
the chromosomes are from phaeodactylum tricornutum and the hints come from some genes predicted by augustus in a previous run with no hints.
Thanks
Rajat
I was using augustus with some hints and I keep getting "No feasible path found in HMM"error message for many combination of these hints. It seems like the HMM mechanism is overfitting the hints and some transition/ emission probabilities might be going to zero. Is there a quick way of fixing this?
I was using the following command:
Code: Select all
augustus --species=generic --hintsfile=augustus_hints.gff --codingseq=on --protein=on chromosomes.fa > aug.gff
Thanks
Rajat