I've been trying to use AUGUSTUS to annotate sections of genome that I know contain single genes (initially validating the protocol with model species with known data). Between running AUGUSTUS on just the gene section with no hints and running it with an MSA and exonpart hints (from BLASTing), all the correct exons are present, but so far I've been unable to get them to all appear in a single transcript.
In order to try and more successfully integrate these outcomes, I want to try to use the MAKER suite, to see if that gives me any better results, but my machine is running out of space - for a fasta file not 60 kbp, MAKER is generating 10 38gb index files before even throwing up any results, and it's taking hours to generate each one. Is this normal, and if not how do I fix it? Running AUGUSTUS on the same stretch didn't even take five minutes (even when cramming it full of extra information).
Any help would be gratefully appreciated.