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

[Duarte Molha]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20121109/f035a619/attachment.html>