[maker-devel] Fwd: all scaffolds failed

[Michael Campbell]

It looks like you are giving the training file from SNAP to genemark, and
that would cause a failure. Try running it with just SNAP and augustus and
see if that fixes the problem.

Thanks,
Mike

On Tue, May 5, 2015 at 1:41 AM, Sunny Sun <solschech at gmail.com> wrote:

>
> Hi,
> I am trying to annotate with Maker a set of 7k scaffolds with a genome
> size of 160Mb. The first run returned 10% of scaffolds FAILED and the
> remaining FINISHED but I didn't get the protein or transcripts fasta files
> so I modified the configuration files accordingly and I am rerunning the
> analysis. So far, all the scaffolds are failing, in the error.log the only
> error I see is of this type for all scaffolds:
>
> error in file format, /tmp/I16VH9JkXG/Q3Pi3DDTOZ_mod
> ERROR: GeneMark Failed
> ERROR: Genemark failed
> --> rank=NA, hostname=sol
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> FAILED CONTIG:scaffold_6
>
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:scaffold_6
>
> examining contents of the fasta file and run log
>
> which doesn't tell me much. I attached the config files. Can someone see
> what is wrong?
>
> Thanks
>
>
>
>
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>
>


-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
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