[ensembl-dev] VEP version 2.7 performance is pitiful when providing parameters from a config file

[Dougherty, Gregory T.]

Thank you, Will, that works.

Was that mentioned somewhere in the documentation?

--
Gregory Dougherty
Sr. Analyst/Programmer | Information Technology
41st Street Professional Building
Ff 3-410-C
(507) 284-8493 | dougherty.gregory at mayo.edu

From: Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>>
Reply-To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Date: Friday, December 21, 2012 11:27 AM
To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Subject: Re: [ensembl-dev] VEP version 2.7 performance is pitiful when providing parameters from a config file

Hi Gregory,

You need a "1" after the cache and offline options in the config file, otherwise that option will be ignored.

cache  1
offline  1

In fact, you don't need to specify both cache and offline, since cache is implied by offline - just offline will do.

Regards and Merry Christmas!

Will McLaren
Ensembl Variation


On 21 December 2012 16:43, Dougherty, Gregory T. <Dougherty.Gregory at mayo.edu<mailto:Dougherty.Gregory at mayo.edu>> wrote:
If I use the attached config file with an installation that has the specified cache file, I get a performance of 1 variant / second on a specific vcf file.  If I run the exact same options from the command line, I get 150+ variants / second.

Why does the config file give such horrible performance?
--
Gregory Dougherty
Sr. Analyst/Programmer | Information Technology
41st Street Professional Building
Ff 3-410-C
(507) 284-8493<tel:%28507%29%20284-8493> | dougherty.gregory at mayo.edu<mailto:dougherty.gregory at mayo.edu>

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