[ensembl-dev] Problem using REST VEP endpoint on pig

mag mr6 at ebi.ac.uk
Tue Dec 9 15:56:24 GMT 2014


Hi Paolo,

Pig only has 19 autosomal chromosomes:
http://www.ensembl.org/Sus_scrofa/Location/Genome

This means there is no chromosome 21, hence you will not be able to 
retrieve any variation consequences on those regions.


Regards,
Magali

On 05/12/2014 14:21, Paolo Cozzi wrote:
>
> Dear all,
>
> Using the new release of REST - VEP endpoint, I got a 400 error code 
> for pig. More precisely, this is the command line I used:
>
> $ curl -H "content-type:application/json" -H "accept:application/json" 
> --data '{ "variants" : ["21 26960070 rs116645811 G A . . .", "21 
> 26965148 rs1135638 G A . . ." ] }' 
> http://rest.ensembl.org/vep/pig/region --verbose
>
> And this is the result:
>
> * About to connect() to rest.ensembl.org port 80 (#0)
> *   Trying 193.62.52.232... connected
> * Connected to rest.ensembl.org (193.62.52.232) port 80 (#0)
> > POST /vep/pig/region HTTP/1.1
> > User-Agent: curl/7.19.7 (x86_64-redhat-linux-gnu) libcurl/7.19.7 
> NSS/3.14.0.0 zlib/1.2.3 libidn/1.18 libssh2/1.4.2
> > Host: rest.ensembl.org
> > content-type:application/json
> > accept:application/json
> > Content-Length: 90
> >
> < HTTP/1.1 400 Bad Request
> < Vary: Content-Type
> < Content-Length: 168
> < Content-Type: application/json
> < X-Runtime: 0.141490
> < X-RateLimit-Limit: 55000
> < X-RateLimit-Reset: 2961
> < X-RateLimit-Period: 3600
> < X-RateLimit-Remaining: 54997
> < Date: Fri, 05 Dec 2014 14:10:39 GMT
> < Connection: close
> <
> * Closing connection #0
> {"error":"Can't call method \"seq_region_Slice\" on an undefined value 
> at 
> /home/ensadmin/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm 
> line 4223.\n"}
>
> Thank you for your support,
>
> Regards,
>
> Paolo
>
>
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