Question: MAKER creating huge index files...
gravatar for dan_adams
2.6 years ago by
dan_adams20 wrote:


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.


ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by dan_adams20

Is MAKER downloading NCBI databases (nt/nr) in the background? 10x38G files sounds suspiciously like that.

ADD REPLYlink written 2.6 years ago by GenoMax94k

Hey @genomax, thanks for the suggestion! I had a look into the files it was creating and it turns out they were all for repeat masking, so I (perhaps dangerously) turned it off. Now it runs in seconds!

ADD REPLYlink written 2.6 years ago by dan_adams20
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