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

[Carson Holt]

If there is a mismatch between the GFF and fasta files, then there was an IO error and a truncated file (not uncommon on NFS), and you need to rerun the contig in question. Before merging all results with gff3_merge and fasta_merge.

—Carson


> On Dec 2, 2016, at 8:10 AM, chebbi mohamed amine <mohamed.amine.chebbi at univ-poitiers.fr> wrote:
> 
> Yes, the GFF3 file generated by maker is missing these ID.
> 
> The master_datastore_index file indicate failed runs on the scaffolds  (scaffold_1710 and scaffold_1734), which could cause the error. 
> 
> I have managed the problem by extracting the missing  ID doing a "grep"  into the gff3 file using  AED and QI statistics and then replace missing ID into the proteinf fasta file like below:
>  
> % map_fasta_ids maker.all.map all.maker.proteins.fasta
>  
> WARNING:  No mapping available for maker-scaffold_1710-augustus-gene-0.3-mRNA-1
>  
> % grep "maker-scaffold_1710-augustus-gene-0.3-mRNA-1" all.maker.proteins.fasta
> >maker-scaffold_1710-augustus-gene-0.3-mRNA-1 protein AED:0.00 eAED:0.00 QI:50|1|1|1|0.66|0.75|4|142|117
>  
> % grep "_AED=0.00;_QI=50|1|1|1|0.66|0.75|4|142|117;_eAED=0.00" maker.gff
>  
> scaffold_1710   maker   mRNA    120513  125092  .       +       .       ID=AV_03422-RA;Parent=AV_03422;Name=AV_03422-RA;Alias=maker-scaffold_1710-augustus-gene-0.23-mRNA-1;_AED=0.00;_QI=50|1|1|1|0.66|0.75|4|142|117;_eAED=0.00;
>  
> # Then, Replace in the all.maker.proteins.fasta  "maker-scaffold_1710-augustus-gene-0.3-mRNA-1" by " maker-scaffold_1710-augustus-gene-0.23-mRNA-1"
> 
> Best, 
> Amine
> 
> De: "chebbi mohamed amine" <mohamed.amine.chebbi at univ-poitiers.fr>
> À: "Carson Holt" <carsonhh at gmail.com>
> Cc: "Maker Mailing List" <maker-devel at yandell-lab.org>
> Envoyé: Mardi 29 Novembre 2016 10:08:56
> Objet: Re: [maker-devel] map_fasta_ids  : No mapping available...
> 
> Yes, the GFF3 file genrated by maker is missing these ID. the master_datastore_index file indicate failed runs on the scaffolds  (scaffold_1710 and scaffold_1734), Which could cause the error. 
> I have managed the problem by extracting the missing  ID doing a grep in to  AED and QI statistics
> De: "Carson Holt" <carsonhh at gmail.com>
> À: "Mohamed Amine Chebbi" <mohamed.amine.chebbi at univ-poitiers.fr>
> Cc: "Maker Mailing List" <maker-devel at yandell-lab.org>
> Envoyé: Lundi 28 Novembre 2016 17:26:40
> Objet: Re: [maker-devel] map_fasta_ids  : No mapping available...
> 
> 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 <mailto: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
> _______________________________________________
> 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
> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20161202/4c5cf52a/attachment-0003.html>