[maker-devel] integrating results from Augustus

[Willett, Christopher S]

Hi All-

I was trying to figure out if it is possible to integrate predictions from the web version of Augustus into a Maker run. I am working on a species of copepod and have a decent set of gene models that I used to train Augustus on its website. That seemed to work okay but I was having trouble figuring out how use these predictions in Maker. I tried generating predictions on the web service and then using the gff file generated from this with the pred_gff option but that doesn’t seem to be working. Is this the best way to do this? It looks like we don’t currently have Augustus installed on our server where I am running these programs.

The problem that I am having with this approach is that each contig is failing and it looks like there are several errors. Including "ERROR: Non-unique top level ID”, "BLAST engine error: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence”, and this chunk:

"ERROR: Failed while prepare section files
ERROR: Chunk failed at level:12, tier_type:3
FAILED CONTIG:Contig149

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:Contig149”


Is there a better way of doing this, perhaps using a different file from the Augustus prediction output?

Thanks for any help you can give me,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: Genome Sciences Building 2252
phone: 919-843-8663
fax: 919-962-1625

http://labs.bio.unc.edu/Willett/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20160613/c611e407/attachment-0002.html>