[ensembl-dev] Error returned when using GRCh37's BioMart MartService

Thomas Maurel maurel at ebi.ac.uk
Tue Jun 2 21:45:33 BST 2015


Dear Bruno,

We experienced a power failure yesterday which affected many of our servers, we brought back most of the Ensembl archive today but I am afraid that the GRCh37 marts are still down at the moment.
All the issues have not been resolved yet so we are still looking into this. In the meantime, you can use our e!75 Ensembl archive on GRCh37.p13: http://feb2014.archive.ensembl.org/index.html <http://feb2014.archive.ensembl.org/index.html>

I will email you as soon as the GRCH37 marts are back online.
Apologies for any inconvenience caused.
Regards,
Thomas 
> On 2 Jun 2015, at 19:53, Bruno Grande <bgrande at sfu.ca> wrote:
> 
> Hello, 
> 
> I'm attempting to download data using GRCh37's BioMart MartService REST API (using XML Query). I've successfully used this exact approach 2-3 months ago. However, my recent attempts return errors. 
> 
> Yesterday, BioMart was down. Now that it's back up, I'm getting the following error:
> 
> Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_80: DBI connect('database=ensembl_mart_80;host=ensdb-5-g-03;port=5637','ensro',...) failed: Can't connect to MySQL server on 'ensdb-5-g-03' (111) at /ensemblweb/grch37/wwwmart/www_80/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98. 
> 
> You may see this error for yourself by visiting this URL (my GET request with the XML query). Note that this only happens when I use the GRCh37 API (http://grch37.ensembl.org/biomart/martservice/), but it works with the latest API (http://www.ensembl.org/biomart/martservice/). 
> 
> Any ideas as to why the GRCh37 API is returning an error? Do you think it has something to do with BioMart being down yesterday? 
> 
> Thanks, 
> Bruno
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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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