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

Will McLaren wm2 at ebi.ac.uk
Tue Oct 7 12:51:51 BST 2014

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 -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 -cache -dir ~/.vep/77/
-force -i example_GRCh38.vcf -plugin Interpro_fixed

In both these cases the VEP will use 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.



On 3 October 2014 16:20, Guillermo Marco Puche <
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_id and
> fetch_by_stable_id methods on Ensembl API.
> Thanks !
> Best regards,
> Guillermo.
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