[maker-devel] integrating results from Augustus

[Carson Holt]

You need to install augustus and place the species parameter files into the …/augustus/config/species directory. They should be downloadable from the augustus online training tool. If you try and use GFF3 from augustus as input instead, you will lose the ability to use evidence alignments to inform the annotations.

—Carson



> On Jun 13, 2016, at 7:01 AM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> 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
> 
> 
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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> Department of Biology
> CB#3280 Coker Hall
> University of North Carolina, Chapel Hill
> Chapel Hill, NC, 27599-3280 
> 
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> 
> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
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