[ensembl-dev] missing ID on call to variant_recoder

Wed Nov 4 14:37:56 GMT 2020

Hi

Sorry there was a typo, the version for the variation database should 
have been 100, i.e. homo_sapiens_variation_100_37

Regards
Helen

On 04/11/2020 14:11, Helen Schuilenburg wrote:
>
> 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/>
>>
>> cid:image001.png at 01D27B05.09A580E0 <http://neogenomics.com/>
>>
>> cid:image002.png at 01D2789A.338CAE00 
>> <https://www.linkedin.com/company/neogenomics-laboratories/>cid:image003.png at 01D2789A.338CAE00 
>> <https://twitter.com/NeoGenomics>cid:image004.png at 01D2789A.338CAE00 
>> <https://www.youtube.com/channel/UCBa0vLyn1ZO7tW-RyJOrxPA>
>>
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