[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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