[ensembl-dev] MySql database setting and configuration.

Helen Schuilenburg helens at ebi.ac.uk
Thu Sep 10 17:05:58 BST 2020


Using a cache is the most efficient way to use VEP. However some VEP 
options require a connection to a database e.g. to look up the position 
when using an identifier (e.g. a dbSNP rsid) or to look up reference 
feature locations.

The Ensembl REST VEP endpoint /vep/human/hgvs should work with a core 
database and an empty variation database provided none of the options 
used require  information from the variation database that is not in the 

The Ensembl REST VEP endpoint /vep/human/id that uses an rsid, does 
require a variation database.

As the number of variants for human have increased loading the MySQL 
database is not trivial. The schema provided uses MyISAM storage engine 
and this is the storage engine on the Ensembl public MySQL Servers.

Did the load using the MyISAM storage engine fail on data import or on 
the index creation?
Is there a particular file/table that caused problems?  I suggest maybe 
trying to load the file in parts.


On 08/09/2020 01:19, Sage Hornung wrote:
> Hi,
> I have asked a few questions recently about setting up an ensemble 
> rest and an ensemble database. I appreciate the all the help.
> I was able to get all the Ensembl data imported after a couple weeks 
> but unfortunately its already corrupted one or more of my InnoDB tables.
> I previously asked I am not opposed to using the cached data and I 
> ended up adding it but one of the rest endpoints supposedly ignores 
> and bypasses the cache. This one in particular 
> https://grch37.rest.ensembl.org/vep/human/hgvs 
> <https://grch37.rest.ensembl.org/vep/human/hgvs>. We are only using a 
> few endpoints and the whole point of this was to speed some of these 
> requests up for ourselves.
> Our MySQL database server has 14GB ram and 4 cores and 2TB of storage. 
> I followed the directions on the Ensembl website for importing the 
> data but the only way I was able to get the larger tables to import 
> was changing the storage engine to InnoDB. Im not sure if this was the 
> best choice because its seems the MyISAM engine is better for read 
> data. But this is the only way I was able to get it to successfully  
> import the data.
> I guess my question is was this a good idea? Is there any specific 
> settings I should be using when configuring MySQL? I have used a few 
> tools online and most say my settings are good/ok doe my 
> configuration. The homo_sapiens_variation_100_37 is the only one 
> that’s giving me issues and only with the tables greater than 25GB. 
> Some of these tables are massive I am looking for any tips or 
> suggestions when dealing with them.
> Thank You,
> Sage Hornung
> *Sage Hornung*
> /Software Engineer /
> *NeoGenomics Laboratories, Inc.*
> 2131 Faraday Avenue, Carlsbad, CA 92008
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