[ensembl-dev] VEP plugin Conservation

[Will McLaren]

You have "offline 1" in your config.

Remove this and you shouldn't see the problem.

Will

On 13 August 2015 at 15:08, Kirsley Chennen <kchennen at unistra.fr> wrote:

> Hi again,
>             The installation of the API went fine, I no longer have the
> instentiation problem. However, I do get an error when using the api:
>
> [15-08-13 15:59:09] kchennen at kc-Dell-XPS-L702X:/opt/apps/bioinfo/ensembl-tools/scripts/variant_effect_predictor
>
> [30:30] > ./variant_effect_predictor.pl --dir cache -i
> example_GRCh37.vcf
>
> 2015-08-13 16:01:17 - Read configuration from cache/vep.ini
> #----------------------------------#
> # ENSEMBL VARIANT EFFECT PREDICTOR #
> #----------------------------------#
>
> version 81
>
> By Will McLaren (wm2 at ebi.ac.uk)
>
> Configuration options:
>
>                    ##
> assembly           GRCh37
> cache              1
> core_type          core
> dir                cache
> dir_plugins        cache/Plugins
> force_overwrite    1
> fork               2
> host               ensembldb.ensembl.org
> input_file         example_GRCh37.vcf
> no_stats           1
> offline            1
> plugin             Conservation,GERP_CONSERVATION_SCORE,mammals
> port               3337
> species            homo_sapiens
> stats              HASH(0x3e68338)
> stats_text         1
> terms              SO
> verbose            1
>
> --------------------
>
> 2015-08-13 16:01:17 - Read existing cache info
> 2015-08-13 16:01:17 - Auto-detected FASTA file in cache directory
> 2015-08-13 16:01:17 - Checking/creating FASTA index
> 2015-08-13 16:02:56 - Loaded plugin: Conservation
> 2015-08-13 16:02:56 - Starting...
> 2015-08-13 16:02:56 - Detected format of input file as vcf
> 2015-08-13 16:02:56 - Read 173 variants into buffer
> 2015-08-13 16:02:56 - Calculating consequences
> [>
> ]    [ 0% ]
> Plugin 'Conservation' went wrong: Can't call method
> "fetch_normalized_slice_projection" on an undefined value at
> /opt/apps/bioinfo/ensembl-api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/ConservationScoreAdaptor.pm
> line 204, <GEN1> line 175.
>
>
>
>
> Thanks
> Kirsley
>
>
>
>
>
> On 13/08/2015 15:46, Will McLaren wrote:
>
> Hi Kirsley,
>
> The only parameter you have to change for GRCh37 is the port, by adding
> "--port 3337" to your VEP command. The plugin will only work when using
> --cache (recommended) or --database; it will not work with --offline.
>
> You also need the ensembl-compara API installed, which is not installed by
> the VEP installer script.
>
> https://github.com/Ensembl/ensembl-compara
>
> http://www.ensembl.org/info/docs/api/api_installation.html
>
> Will
>
> On 13 August 2015 at 14:36, Kirsley Chennen <kchennen at unistra.fr> wrote:
>
>> Hi Will,
>>             Am still having the same issue with the latest version of the
>> Convervation.pm plugin :
>>
>> 2015-08-13 15:31:17 - Failed to instantiate plugin Conservation: Failed
>> to connect to compara database
>>
>>
>> Do we have to the config for the database in the vep.ini file?
>>
>>     # reconnect to DB without species param
>>     my $config = $self->{config};
>>     $reg->load_registry_from_db(
>>         -host       => $config->{host},
>>         -user       => $config->{user},
>>         -pass       => $config->{password},
>>         -port       => $config->{port},
>>         -db_version => $config->{db_version},
>>         -no_cache   => $config->{no_slice_cache},
>>     );
>>
>> If that's so, what are the parameters for the GRCh37 human assembly?
>>
>> Regards
>> Kirsley
>>
>>
>>
>> On 13/08/2015 14:46, Will McLaren wrote:
>>
>> Hi Guillermo,
>>
>> Thanks for the report, I've pushed a fix to the plugin on GitHub.
>>
>> Regards
>>
>> Will
>>
>> On 13 August 2015 at 12:36, Guillermo Marco Puche <
>> guillermo.marco at sistemasgenomicos.com> wrote:
>>
>>> Dear devs,
>>>
>>> I'm using latest version of VEP Conservation plugin available in github.
>>> However it's not working for me:
>>>
>>> 2015-08-13 13:35:17 - Failed to instantiate plugin Conservation: Failed
>>> to connect to compara database
>>>
>>> Is this a bug?
>>>
>>> Regards,
>>> Guillermo.
>>>
>>>
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>>
>>
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>
>
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