[ensembl-dev] Error running example files in VEP 2.7 - script dies in VEP.pm line 1064.

Will McLaren wm2 at ebi.ac.uk
Fri Nov 9 14:07:09 GMT 2012


Hi Duarte,

--debug (debug => 1 in your config) is not for external use

Will


On 9 November 2012 14:02, Duarte Molha <Duarte.Molha at ogt.co.uk> wrote:

> Dear Developers****
>
> ** **
>
> Just tried running the example files using the latest script with what I
> consider to be pretty standard config file and it dies at VEP.pm line 1064.
> ****
>
> ** **
>
> Here is the output:****
>
> ** **
>
> perl variant_effect_predictor.pl --config vep_custom.ini -i example.vcf
> --debug****
>
> 2012-11-09 14:01:17 - Read configuration from vep_custom.ini****
>
> #----------------------------------#****
>
> # ENSEMBL VARIANT EFFECT PREDICTOR #****
>
> #----------------------------------#****
>
> ** **
>
> version 2.7****
>
> ** **
>
> By Will McLaren (wm2 at ebi.ac.uk)****
>
> ** **
>
> Configuration options:****
>
> ** **
>
> buffer_size        50000****
>
> cache              1****
>
> check_existing     1****
>
> config             vep_custom.ini****
>
> core_type          core****
>
> debug              1****
>
> dir                /ReferenceData/vep_cache/****
>
> force_overwrite    1****
>
> gmaf               1****
>
> host               ensembldb.ensembl.org****
>
> input_file         example.vcf****
>
> plugin
> Condel,/ReferenceData/vep_cache/Plugins/config/Condel/config,b****
>
> polyphen           b****
>
> port               5306****
>
> protein            1****
>
> regulatory         1****
>
> sift               b****
>
> species            homo_sapiens****
>
> terms              display****
>
> toplevel_dir       /ReferenceData/vep_cache/****
>
> verbose            1****
>
> ** **
>
> --------------------****
>
> ** **
>
> Will only load v69 databases****
>
> Species 'homo_sapiens' loaded from database 'homo_sapiens_core_69_37'****
>
> Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_69_37'****
>
> Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_69_37'****
>
> Species 'homo_sapiens' loaded from database
> 'homo_sapiens_otherfeatures_69_37'****
>
> Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_69_37'***
> *
>
> homo_sapiens_variation_69_37 loaded****
>
> homo_sapiens_funcgen_69_37 loaded****
>
> Bio::EnsEMBL::Compara::DBSQL::DBAdaptor not found so the following compara
> databases will be ignored: ensembl_compara_69****
>
> ensembl_ancestral_69 loaded****
>
> ensembl_ontology_69 loaded****
>
> 2012-11-09 14:01:18 - Connected to core version 69 database and variation
> version 69 database****
>
> 2012-11-09 14:01:18 - Read existing cache info****
>
> 2012-11-09 14:01:18 - Loaded plugin: Condel****
>
> 2012-11-09 14:01:18 - Starting...****
>
> 2012-11-09 14:01:18 - Detected format of input file as vcf****
>
> 2012-11-09 14:01:18 - Read 173 variants into buffer****
>
> 2012-11-09 14:01:18 - Reading transcript data from cache and/or database**
> **
>
> [====================================================================================================================================================================]
> [ 100% ]****
>
> 2012-11-09 14:01:19 - Retrieved 3090 transcripts (0 mem, 3176 cached, 0
> DB, 86 duplicates)****
>
> 2012-11-09 14:01:19 - Reading regulatory data from cache and/or database**
> **
>
> [====================================================================================================================================================================]
> [ 100% ]****
>
> 2012-11-09 14:01:19 - Retrieved 13706 regulatory features (0 mem, 13710
> cached, 0 DB, 4 duplicates)****
>
> 2012-11-09 14:01:19 - Checking for existing variations****
>
> [====================================================================================================================================================================]
> [ 100% ]****
>
> 2012-11-09 14:01:23 - Analyzing chromosome 21****
>
> 2012-11-09 14:01:23 - Analyzing variants****
>
> [====================================================================================================================================================================]
> [ 100% ]****
>
> 2012-11-09 14:01:23 - Analyzing RegulatoryFeatures****
>
> [====================================================================================================================================================================]
> [ 100% ]****
>
> 2012-11-09 14:01:23 - Analyzing MotifFeatures****
>
> [====================================================================================================================================================================]
> [ 100% ]****
>
> 2012-11-09 14:01:23 - Calculating consequences****
>
> [====================================================================================================================================================================]
> [ 100% ]****
>
> 2012-11-09 14:01:24 - Analyzing chromosome 22****
>
> 2012-11-09 14:01:24 - Analyzing variants****
>
> [====================================================================================================================================================================]
> [ 100% ]****
>
> 2012-11-09 14:01:24 - Analyzing RegulatoryFeatures****
>
> [====================================================================================================================================================================]
> [ 100% ]****
>
> 2012-11-09 14:01:24 - Analyzing MotifFeatures****
>
> [====================================================================================================================================================================]
> [ 100% ]****
>
> 2012-11-09 14:01:24 - Calculating consequences****
>
> [====================================================================================================================================================================]
> [ 100% ]****
>
> Undefined subroutine &Bio::EnsEMBL::Variation::Utils::VEP::total_size
> called at
> /NGS_Test/duarte/VEP_27_testing/Bio/EnsEMBL/Variation/Utils/VEP.pm line
> 1064.****
>
> ** **
>
> Can you tell me what might be wrong?****
>
> Cheers****
>
> ** **
>
> Duarte Molha****
>
> ** **
>
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