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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Dear Developers<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Here is the output:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>perl variant_effect_predictor.pl --config vep_custom.ini -i example.vcf --debug<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:17 - Read configuration from vep_custom.ini<o:p></o:p></p><p class=MsoNormal>#----------------------------------#<o:p></o:p></p><p class=MsoNormal># ENSEMBL VARIANT EFFECT PREDICTOR #<o:p></o:p></p><p class=MsoNormal>#----------------------------------#<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>version 2.7<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>By Will McLaren (wm2@ebi.ac.uk)<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Configuration options:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>buffer_size 50000<o:p></o:p></p><p class=MsoNormal>cache 1<o:p></o:p></p><p class=MsoNormal>check_existing 1<o:p></o:p></p><p class=MsoNormal>config vep_custom.ini<o:p></o:p></p><p class=MsoNormal>core_type core<o:p></o:p></p><p class=MsoNormal>debug 1<o:p></o:p></p><p class=MsoNormal>dir /ReferenceData/vep_cache/<o:p></o:p></p><p class=MsoNormal>force_overwrite 1<o:p></o:p></p><p class=MsoNormal>gmaf 1<o:p></o:p></p><p class=MsoNormal>host ensembldb.ensembl.org<o:p></o:p></p><p class=MsoNormal>input_file example.vcf<o:p></o:p></p><p class=MsoNormal>plugin Condel,/ReferenceData/vep_cache/Plugins/config/Condel/config,b<o:p></o:p></p><p class=MsoNormal>polyphen b<o:p></o:p></p><p class=MsoNormal>port 5306<o:p></o:p></p><p class=MsoNormal>protein 1<o:p></o:p></p><p class=MsoNormal>regulatory 1<o:p></o:p></p><p class=MsoNormal>sift b<o:p></o:p></p><p class=MsoNormal>species homo_sapiens<o:p></o:p></p><p class=MsoNormal>terms display<o:p></o:p></p><p class=MsoNormal>toplevel_dir /ReferenceData/vep_cache/<o:p></o:p></p><p class=MsoNormal>verbose 1<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>--------------------<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Will only load v69 databases<o:p></o:p></p><p class=MsoNormal>Species 'homo_sapiens' loaded from database 'homo_sapiens_core_69_37'<o:p></o:p></p><p class=MsoNormal>Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_69_37'<o:p></o:p></p><p class=MsoNormal>Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_69_37'<o:p></o:p></p><p class=MsoNormal>Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_69_37'<o:p></o:p></p><p class=MsoNormal>Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_69_37'<o:p></o:p></p><p class=MsoNormal>homo_sapiens_variation_69_37 loaded<o:p></o:p></p><p class=MsoNormal>homo_sapiens_funcgen_69_37 loaded<o:p></o:p></p><p class=MsoNormal>Bio::EnsEMBL::Compara::DBSQL::DBAdaptor not found so the following compara databases will be ignored: ensembl_compara_69<o:p></o:p></p><p class=MsoNormal>ensembl_ancestral_69 loaded<o:p></o:p></p><p class=MsoNormal>ensembl_ontology_69 loaded<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:18 - Connected to core version 69 database and variation version 69 database<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:18 - Read existing cache info<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:18 - Loaded plugin: Condel<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:18 - Starting...<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:18 - Detected format of input file as vcf<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:18 - Read 173 variants into buffer<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:18 - Reading transcript data from cache and/or database<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:19 - Retrieved 3090 transcripts (0 mem, 3176 cached, 0 DB, 86 duplicates)<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:19 - Reading regulatory data from cache and/or database<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:19 - Retrieved 13706 regulatory features (0 mem, 13710 cached, 0 DB, 4 duplicates)<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:19 - Checking for existing variations<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:23 - Analyzing chromosome 21<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:23 - Analyzing variants<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:23 - Analyzing RegulatoryFeatures<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:23 - Analyzing MotifFeatures<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:23 - Calculating consequences<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:24 - Analyzing chromosome 22<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:24 - Analyzing variants<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:24 - Analyzing RegulatoryFeatures<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:24 - Analyzing MotifFeatures<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>2012-11-09 14:01:24 - Calculating consequences<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Can you tell me what might be wrong?<o:p></o:p></p><p class=MsoNormal>Cheers<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Duarte Molha</span><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>