[ensembl-dev] VEP plugin errors on Ensembl 76+

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Fri Oct 10 10:27:53 BST 2014


Hi Will,

I'm querying local Ensembl DB (76, GRCh38).
As you said maybe the problem is due to downloaded cache, on previous 
releases I had only one cache as there was only on human assembly available.
For release 76 I've the following two directories with their respective 
caches:

  * /share/references/vep/homo_sapiens/76_GRCh38/
  * /share/references/vep/homo_sapiens/76_GRCh37/

I'm using these options related to cache when using VEP script:
dir_cache          /share/references/vep
assembly           GRCh38

I wasn't using assembly flag until this vep release. I thought I could 
have both caches and switch between them with assembly flag. Anyways, 
maybe the problem is in directory structure, and GRCh37/GRCh38 
directories should be on same level inside "76" directory.

I guess having the correct directory structure will solve the problem.

Regards,
Guillermo.

On 07/10/14 13:51, Will McLaren wrote:
> Hi Guillermo,
>
> I suspect the issue is to do with database connections.
>
> If you are running your plugin with the VEP in offline mode 
> (--offline), then you will be unable to retrieve data from the 
> databases without instantiating your own registry instance and 
> adaptors within the plugin.
>
> If you are running the VEP using --cache or --database you shouldn't 
> have this issue; just make sure that your cache version and the 
> version of the database you are connecting to match, and that the 
> assemblies also match.
>
> If I run, for example:
>
> perl -I vep_plugins/ variant_effect_predictor.pl 
> <http://variant_effect_predictor.pl> -cache -port 3337 -dir 
> ~/.vep/77/GRCh37/ -force -i example_GRCh37.vcf -plugin Interpro_fixed
>
> it runs without an issue. Or similarly for the GRCh38 example:
>
> perl -I vep_plugins/ variant_effect_predictor.pl 
> <http://variant_effect_predictor.pl> -cache -dir ~/.vep/77/ -force -i 
> example_GRCh38.vcf -plugin Interpro_fixed
>
> In both these cases the VEP will use ensembldb.ensembl.org 
> <http://ensembldb.ensembl.org> to retrieve data; the first example 
> uses port 3337 to connect to the GRCh37 mirror, and the second the 
> default (3306) port to connect to the latest GRCh38 mirror.
>
> HTH
>
> Will
>
> On 3 October 2014 16:20, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     Dear developers,
>
>     I'm experiencing some VEP plugin errors on Ensembl 76+.
>
>     I've uploaded both plugins failing to this public repository:
>     https://github.com/guillermomarco/vep_plugins
>
>     I've been looking for API changes in
>     http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Utils_1_1BaseVepPlugin.html#a2d966d465a2bbc2a067417cc4978e304
>     but I can't really find why I'm getting the following errors:
>
>     Plugin 'Interpro_fixed' went wrong: Can't call method "translation" on an undefined value at Interpro_fixed.pm line 107
>
>     Plugin 'Gene_description' went wrong: Can't call method "description" on an undefined value at Gene_description.pm line 78.
>
>
>     It's like hashes are empty:
>
>     $gene = $config->{ga}->fetch_by_transcript_stable_id($transcript_id);
>
>     	$gene_desc = $gene->description;
>
>
>     my $slice_adaptor =
>     $config->{reg}->get_adaptor(($config->{species}), 'core',
>     'Transcript');
>
>     	my $tr = $slice_adaptor->fetch_by_stable_id($Transcript);
>
>     	my $translation = $tr->translation;
>
>
>     I suspect of $config->{ga} and $config->{reg} are the cause of
>     this problem, because I still see fetch_by_transcript_stable_idand
>     fetch_by_stable_idmethods on Ensembl API.
>
>     Thanks !
>
>
>     Best regards,
>     Guillermo.
>
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