[maker-devel] cds error

[Carson Holt]

You can upload your GFF3 file here, and I can take a look —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi

My guess is that either gffread is not translating it correctly or you used your own GFF3 as input to maker during a run. If a gff3 submited data to MAKER has partially overlapping exons in a gene prediction, MAKER can’t fix it, and you get back whatever translation came from the gff3.

—Carson


> On Nov 28, 2021, at 9:20 PM, zc y <prometheus07.06 at gmail.com> wrote:
> 
> Dear  Maker developers,
> I found a CDS error in my rice project. I ran the maker (3.01.03) and it finished without error in master_datastore_index.log. But when I use gffread to translate the protein from maker gff, I found that almost all of proteins are not start with 'M' and many stop codons in it. 
> In fact, I checked the protein file (Chr12.maker.proteins.fasta) provided by the maker, it is correct. 
> I used the same parameter and evidence in another rice, it don't have the problem.
> What should I do?
> 
> 
> thanks,
> <QQ截图20211129121755.png><QQ截图20211129121917.png>
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