[ensembl-dev] Error running example files in VEP 2.7 - script dies in VEP.pm line 1064.
Duarte Molha
Duarte.Molha at ogt.co.uk
Fri Nov 9 14:14:31 GMT 2012
Yes... I saw that just after sending the email... I forgot the parameter I wanted was verbose!
My apologies :)
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 09 November 2012 14:07
To: Ensembl developers list
Subject: Re: [ensembl-dev] Error running example files in VEP 2.7 - script dies in VEP.pm line 1064.
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<mailto: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<http://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<mailto: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<http://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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