[maker-devel] Error trying to submit genome to ncbi

[Daniel Ence]

Hi Emmanuel, Please “reply all” to in these exchanges so that they’ll stay stored on the maker-devel list for others to find in the future. It also helps keep the conversation open so that others can chime in and help out too. :) 

I looked at several of the “nonfunctional due to frameshift” genes and they have associated features in the gff3 file. So there might be a frameshift issue in the original annotations, but I’d doubt that, or a frameshift error might be getting introduced when you convert to the tbl format. 


> On Nov 2, 2017, at 5:12 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Daniel
> 
> I NCBI first complained of this even when I hadn't used GAG annotation to remove N's,
> 
> On my raw file they complained about this
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> On Thu, Nov 2, 2017 at 10:07 PM, Daniel Ence <dandence at gmail.com <mailto:dandence at gmail.com>> wrote:
> Hi Emmanuel, I recommend looking into what Carson suggested. If you edited the fasta files for the “NNN” characters for the transcripts or reference genome and then resubmitted without changing the gff3 coordinates, then that would result in these kind of errors. 
> 
> ~Daniel
> 
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>> On Nov 2, 2017, at 5:02 PM, Emmanuel Nnadi <eennadi at gmail.com <mailto:eennadi at gmail.com>> wrote:
>> 
>>  muc_functional.blast.gff <https://drive.google.com/file/d/1rPSI3HhceRuJMzWO9hAej-BzMNUSKz7g/view?usp=drive_web>
> 

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