[ensembl-dev] missing ID on call to variant_recoder

Wed Nov 4 14:11:21 GMT 2020

Hi

 From the log provided the database homo_sapiens_variation_100_37 is not 
being loaded.

This database is used by the variant_recoder to return the id.

 From the logs homo_sapiens_core_100_37 is loaded.

Please can you check that the homo_sapiens_variation_101_37 can be 
accessed using the configuration
provided in ensembl_rest.conf  (Model::Registry section) and used to 
access homo_sapiens_core_100_37

The variation database can also be queried to check that the id in the 
local variation database e.g.

select v.name
from variation v, variation_feature vf
where v.variation_id = vf.variation_id
and name = 'rs80358450';

name: rs80358450
1 row in set (0.25 sec)

Regards
Helen

On 03/11/2020 17:16, Sage Hornung wrote:
>
> Hi,
>
> I am making the following call (To localhost though not Ensembl) 
>  http://grch37.rest.ensembl.org 
> /variant_recoder/human/13:g.32893310A>G?content-type=application/json&fields=hgvsg,id 
> <%20http:/grch37.rest.ensembl.org%20/variant_recoder/human/13:g.32893310A%3eG?content-type=application/json&fields=hgvsg,id> 
> to a local ensemble setup. But I don’t get an ID back in the response. 
> I loaded the ensembl_stable_ids_100 database but its was the one I 
> found here ftp://ftp.ensembl.org/pub/release-100/mysql/ 
> <ftp://ftp.ensembl.org/pub/release-100/mysql/>.
>
> Here is what I get back using my local Ensembl  REST and Ensembl   DB 
> . If I change to your DB it gives the ID back. Any idea what I am 
> going wrong? Or how this should be configured differently? I am making 
> my changes in the  ensembl_rest.conf file
>
> [
>
>     {
>
> "hgvsg": [
>
> "NC_000013.10:g.32893310A>G",
>
> "LRG_293:g.8694A>G"
>
>         ],
>
> "input": "13:g.32893310A>G"
>
>     }
>
> ]
>
> I do see that pointing to the ensemble DB gives this when starting up 
> the REST server
>
> Species 'homo_sapiens' loaded from database 'homo_sapiens_core_100_37'
>
> Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_100_37'
>
> Species 'homo_sapiens' loaded from database 
> 'homo_sapiens_otherfeatures_100_37'
>
> Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_100_37'
>
> homo_sapiens_variation_100_37 loaded
>
> homo_sapiens_funcgen_100_37 loaded
>
> ensembl_compara_100 loaded
>
> No ancestral database found
>
> ensembl_ontology_100 loaded
>
> No taxonomy database found
>
> No ensembl_metadata database found
>
> No production database or adaptor found
>
> ensembl_stable_ids_100 loaded
>
> But it only finds the homo_sapiens_core DB when I point to my local DB 
> (I definitely have the variation DB loaded )
>
> Will only load v100 databases
>
> Species 'homo_sapiens' loaded from database 'homo_sapiens_core_100_37'
>
> No variation databases found
>
> No funcgen databases found
>
> No Compara databases found
>
> No ancestral database found
>
> No ontology database found
>
> No taxonomy database found
>
> No ensembl_metadata database found
>
> No production database or adaptor found
>
> *Sage Hornung*
>
> /Software Engineer /
>
> *NeoGenomics Laboratories, Inc.*
>
> 2131 Faraday Avenue, Carlsbad, CA 92008
>
> *Phone: *760.516.5114
>
> *Cell: *760.755.3930
>
> sage.hornung at neogenomics.com <mailto:sage.hornung at neogenomics.com>
>
> neogenomics.com <http://neogenomics.com/>
>
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>
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>
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