basically I just want to train augustus (ab initio gene predictor) with AutoAug.pl but I always end up with the same error (scipio is not installed or not in your path) . Luckly I found someone who has the same problem like me (https://www.biostars.org/p/210670/). He suggested to run scipio by it's own. I have done it, but scipio does not produce any output files. Usually scipio should create a yaml file that I can use for augustus training by converting it.
Scipio only gives me a terminal output (last lines):
### not found: xyz[1...8], vwx[413-420],...
### end of Scipio output
I suppose the terminal output is the yaml file but i don't see any options to save it. Do I have to save it manually? Does it make sense to filter my protein files to avoid getting the error "### not found ..."?
Thanks alot in advance