[maker-devel] map_fasta_ids : No mapping available...

[Carson Holt]

The map file you run with is two columns (old_id and new_id). If the input file has IDs that do not match anything in the old_id column then it throws the warning. It means there is a mismatch between the map file being used and the fasta file.  This can occur if you did downstream manipulation of the fasta file, are using the wrong fasta file, or if you used GFF3 as input to a maker step that as generated an ID mismatch.

—Carson



> On Nov 24, 2016, at 2:45 PM, Mohamed Amine Chebbi <mohamed.amine.chebbi at univ-poitiers.fr> wrote:
> 
> Hello !
> 
> I'am attempting to rename genes of maker.proteins.fasta for Genebank submission using the map_fasta_ids script. It seems to work correctly for the major of gene models, except to those ones having the below warning message  :
> 
> WARNING: No mapping available for maker-scaffold_1710-augustus-gene-0.3-mRNA-1
> WARNING: No mapping available for maker-scaffold_1710-augustus-gene-0.0-mRNA-1
> WARNING: No mapping available for maker-scaffold_1710-snap-gene-0.6-mRNA-1
> WARNING: No mapping available for maker-scaffold_1710-augustus-gene-0.4-mRNA-1
> WARNING: No mapping available for maker-scaffold_1734-augustus-gene-0.1-mRNA-1
> WARNING: No mapping available for maker-scaffold_1734-augustus-gene-0.2-mRNA-1
> WARNING: No mapping available for maker-scaffold_1734-augustus-gene-0.0-mRNA-1
> WARNING: No mapping available for maker-scaffold_1734-augustus-gene-0.5-mRNA-1
> WARNING: No mapping available for maker-scaffold_1734-augustus-gene-0.6-mRNA-1
> WARNING: No mapping available for maker-scaffold_1734-snap-gene-0.15-mRNA-1
> WARNING: No mapping available for maker-scaffold_1734-snap-gene-0.16-mRNA-1
> 
> Looking into the maker.gff file, these gene names are missing  and may be replaced by other ones which differ by the numbers following the gene predictor.
> 
> I wounder if you can explain me the reason of these warning message and how to resolve it.
> 
> Thank you ,
> 
> Best,
> Amine
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