[ensembl-dev] VEP plugin Conservation
Kirsley Chennen
kchennen at unistra.fr
Thu Aug 13 15:08:41 BST 2015
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
> <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.
>>
>>
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