[ensembl-dev] VEP API returning 400 for memory error

[Anja Thormann]

Hi Asier,

I would like to take a look at your script please. I recommend for the first part that you use our VEP POST endpoints for region <https://rest.ensembl.org/documentation/info/vep_region_post> and id <https://rest.ensembl.org/documentation/info/vep_id_post>. At this point I recommend that you rerun your requests a few times on a 400 error and if the requests keep failing contact us with details (variant id or region) of your failed requests. Can you rule out that the error message has a 429 code due to too many requests?

Thank you,
Anja

> On 21 Aug 2019, at 14:28, Asier Gonzalez <gonzaleza at ebi.ac.uk> wrote:
> 
> Hello Anja,
> 
> Thank you for your email. This is an script that calls both the id (/vep/human/id/) and region (/vep/human/region/) endpoints depending on whether the variant is defined by a rsID or a genomic coordinates. It calls the API thousands of times using GET requests, once per variant. I don't see any other settings but I can point you to the few code lines that control it on Github if you want to have a look yourself.
> 
> Please let me know if I can help. I just need to know whether this is an expected behaviour as our script retries calling the API if the response is a 5XX error but it passes if it's a 400 as it should have been caused by the query and retrying should not make any difference.
> 
> Best wishes,
> Asier
> 
> On 21/08/2019 13:39, Anja Thormann wrote:
>> Dear Asier,
>> 
>> thank you for your feedback. Could you please let me know which VEP endpoint and settings you use? If you are using a POST endpoint, how many variant ids or regions are you sending? I assume that the problem happens at a point during the VEP calculation where it is difficult to differentiate the cause of the problem. But we will investigate further and hopefully be able to provide a more accurate error report.
>> 
>> Best wishes,
>> Anja
>> 
>>> On 21 Aug 2019, at 12:47, Asier Gonzalez <gonzaleza at ebi.ac.uk> wrote:
>>> 
>>> Hi,
>>> 
>>> I have an script that calls the VEP API for a few thousand variants and does some processing. The script captures HTTP errors and messages and I have found a few cases where the 400 error is accompanied by a  "ERROR: Cannot allocate memory" message. If I query the API again with the ids that produced that error I get a results so I understand that this is a temporary issue. I could handle the 400 errors further to control these cases but I wonder if it is an expected case or if it an issue as it sounds as this should be an 5XX error instead of a 400.
>>> 
>>> Kind regards,
>>> Asier
>>> 
>>> 
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