[ensembl-dev] VEP plugin Conservation
Kirsley Chennen
kchennen at unistra.fr
Thu Aug 13 15:44:45 BST 2015
Oups! My mistake! Works like a charm now. However, it seems rather slow
with the database connection. I've just tested an alternative which
looks much faster by using the bigwig file with the custom annotation
option. My question is do we get the same results for indel if we do the
average of the values returned by "overlap" annotation type parameter?
Thanks
Kirsley
On 13/08/2015 16:19, Will McLaren wrote:
> 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
> <mailto: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
> <http://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 <mailto: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 <http://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
>> <mailto: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
>>> <mailto: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.
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing listDev at ensembl.org <mailto:Dev at ensembl.org>
>>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog:http://www.ensembl.info/
>>
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>>
>>
>> _______________________________________________
>> Dev mailing listDev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog:http://www.ensembl.info/
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150813/7998e228/attachment.html>
More information about the Dev
mailing list