[maker-devel] genes longer than contig in maker

[Carson Holt]

1. You have two contigs with the same ID in your assembly (one longer and one shorter).
2. Your BioPerl index for retrieving the sequence is corrupt somehow. Requires delete of previous output directory before restarting.
3. You are using bad formatted GFF3 as input into maker, and it is somehow not failing right away.


The fact you get output means that it was able to translate the sequence into protein with CDS etc. So it was not too short for that. Look at the contig line in the GFF3 to get the length of the contig maker is seeing to compare to the feature positions given.

—Carson


> On Feb 23, 2017, at 5:40 AM, lucile.soler at bils.se wrote:
> 
> Hello,
> 
>  I am using maker3 to annotate a lizard.
> 
> 
> The maker part went well but then when I want to do the functional annotation, it seems that for some contigs maker has created genes outside of the contig size.
> 
>  For instance :
> 
> 
>  XXX1   maker gene    2          26717            .           -           .           ID=maker-XXX1_pilon-augustus-gene-0.8;Name=maker-XXX1_pilon-augustus-gene-0.8
> 
> 
> XXX1   maker mRNA 2          26717            .           -           .           ID=maker- XXX1_pilon-augustus-gene-0.8-mRNA-1;Parent=maker-XXX1_pilon-augustus-gene-0.8;Name=maker-XXX1_pilon-augustus-gene-0.8-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|0.8|0.5|1|0.4|0.33|6|5291|105
> 
> XXX1   maker mRNA 2          26717            .           -           .           ID=maker-XXX1_pilon-augustus-gene-0.8-mRNA-2;Parent=maker-XXX1_pilon-augustus-gene-0.8;Name=maker-XXX1_pilon-augustus-gene-0.8-mRNA-2;_AED=0.08;_eAED=0.08;_QI=0|0.5|0.4|1|0.25|0.4|5|4442|170
> 
> and the length of the contig is 26696
> 
> 
>  
> 
> Any idea of what could have happened? Have you seen that already?
> 
>  
> 
> Let me know what more information you need to answer.
> 
> Thank you very much for your help,
> 
> 
> 
> 
> 
> Lucile Soler
> 
> PhD in Bioinformatics
> Genome Annotation Platform
> NBIS (National Bioinformatics Infrastructure Sweden)
> mail:lucile.soler at bils.se <http://bils.se/>
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