[maker-devel] Error: Chunk failed at level

[Jason Stajich]

Hi Ian - 

Do you get any gene models if you run RM or SNAP on these directly?  I can't tell if this means there is no overlap between your different prediction sets or if you didn't get ab initio predictions?

Jason
On Mar 8, 2012, at 6:15 AM, Ian Misner wrote:

> Hello,
> 
> I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some very large contigs that haven't annotated any proteins.  I have looked through the output from the run and of the 74 contigs that failed I only have three errors.
> 
> They are Chunk failed at level 3, 8, & 16
> 
> What are those errors?  How can I get the annotations for these failed runs to work?  I have the entire output if you would need to see that file.  In my opts ctl file I set it to retry failed contigs 2 times and do a fresh run each time.  All 74 contigs failed all 3 attempts to run.  Any help would be much appreciated.
> 
> Cheers
> Ian
> 
> 
> *************************************
> Mr. Ian Misner
> PhD. Candidate
> Department of Biological Sciences
> University of Rhode Island
> 120 Flagg Road
> Kingston, RI 02881
> Office: CBLS 260
> Ph: 1-401-874-9726
> fax (401) 874-2065
> ianmisner at my.uri.edu
> http://cels.uri.edu/bio/lanelab/  
> 
> 
> 
> 
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> 
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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