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

[Daniel Ence]

Hi, Thank you for sending me your data, but which ones are the offending genes that NCBI is complaining about? Can you identify the problem that NCBI is giving in some subset of the gene features? 

~Daniel




> On Nov 2, 2017, at 4:20 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Daniel thanks for your reply.
> 
> I have attached my .tbl file
> 
> you would see 
> <77753	>77549	gene
> 			locus_tag	CR513_00193
> 			gene	AtMg00820
> 			note	nonfunctional due to frameshift
> 
> 
> Is another example.
> 
> Its becoming frustrating.
> 
> I have not posted the two errors before 
> [1] Please remove any N nucleotides from the beginning or end of the sequence.
> 
> [2] No feature should begin or end inside a gap.  Instead the feature should
> be made partial at the gap boundary.
> 
> [3] Coding regions should not be 5' partial if they begin with the start
> methionine.  If this is an internal methionine int he translation than
> it is fine if they are partial.  Conversely, all coding regions
> must have a stop codon or be 3' partial.
> 
> 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 9:08 PM, Daniel Ence <dandence at gmail.com <mailto:dandence at gmail.com>> wrote:
> Hi, I think you’ve posted before about issues 1 and 2 from the NCBI. The note for issue 3 from NCBI sounds like there are gene features that don’t have associated transcript, CDS or exon features. I’m not certain how that could be a result from MAKER. It might be something that someone else created (manually or with another tool), and then passed to maker from a GFF file. In the example included in your email, it looks like these offending genes are transposons that have been annotated as genes. If that is the case for the rest of the offending genes, then I would suggest changing the “type” field (column 3) from “gene” to something else, like “transposable_element” perhaps. 
> 
> ~Daniel
> 
> 
>> On Nov 2, 2017, at 3:51 PM, Emmanuel Nnadi <eennadi at gmail.com <mailto:eennadi at gmail.com>> wrote:
>> 
>> Hi,
>> 
>> I am trying to submit my genome i annotated using maker and they sent back this error,
>> 1. Please remove any N nucleotides from the beginning or end of the sequence
>>  2.No feature should begin or end inside a gap.  Instead the feature should
>> be made partial at the gap boundary.
>> 
>> [3] Coding regions should not be 5' partial if they begin with the start
>> methionine.  If this is an internal methionine int he translation than
>> it is fine if they are partial.  Conversely, all coding regions
>> must have a stop codon or be 3' partial.
>> You have a large number of gene features that are not associated
>> with other features.  Please include on these features in the
>> gene description field some description of what the gene would
>> have encoded.
>> 
>> A feature table example of this is:
>> 
>> <41156  >40652  gene
>>                         gene_desc       transposon
>>                         locus_tag       CR513_45338
>>                         note    nonfunctional due to frameshift
>> Please how can i use maker to solve this problem?
>> 
>> 
>> 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>_______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 
> <combined_5001-10000.tbl>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20171102/b16304bf/attachment-0003.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1356 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20171102/b16304bf/attachment-0003.p7s>