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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Yes... I saw that just after sending the email... I forgot the parameter I wanted was verbose!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>My apologies </span><span style='font-size:11.0pt;font-family:Wingdings;color:#1F497D'>J</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='margin-left:36.0pt'><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Will McLaren<br><b>Sent:</b> 09 November 2012 14:07<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] Error running example files in VEP 2.7 - script dies in VEP.pm line 1064.<o:p></o:p></span></p></div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><div><p class=MsoNormal style='margin-left:36.0pt'>Hi Duarte,<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><p class=MsoNormal style='margin-left:36.0pt'>--debug (debug => 1 in your config) is not for external use<o:p></o:p></p><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>Will<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt'><o:p> </o:p></p><div><p class=MsoNormal style='margin-left:36.0pt'>On 9 November 2012 14:02, Duarte Molha <<a href="mailto:Duarte.Molha@ogt.co.uk" target="_blank">Duarte.Molha@ogt.co.uk</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Dear Developers<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Here is the output:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --config vep_custom.ini -i example.vcf --debug<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:17 - Read configuration from vep_custom.ini<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>#----------------------------------#<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'># ENSEMBL VARIANT EFFECT PREDICTOR #<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>#----------------------------------#<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>version 2.7<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>By Will McLaren (<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Configuration options:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>buffer_size 50000<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>cache 1<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>check_existing 1<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>config vep_custom.ini<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>core_type core<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>debug 1<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>dir /ReferenceData/vep_cache/<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>force_overwrite 1<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>gmaf 1<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>host <a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>input_file example.vcf<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>plugin Condel,/ReferenceData/vep_cache/Plugins/config/Condel/config,b<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>polyphen b<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>port 5306<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>protein 1<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>regulatory 1<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>sift b<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>species homo_sapiens<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>terms display<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>toplevel_dir /ReferenceData/vep_cache/<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>verbose 1<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>--------------------<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Will only load v69 databases<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Species 'homo_sapiens' loaded from database 'homo_sapiens_core_69_37'<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_69_37'<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_69_37'<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_69_37'<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_69_37'<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>homo_sapiens_variation_69_37 loaded<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>homo_sapiens_funcgen_69_37 loaded<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>ensembl_ancestral_69 loaded<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>ensembl_ontology_69 loaded<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:18 - Read existing cache info<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:18 - Loaded plugin: Condel<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:18 - Starting...<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:18 - Detected format of input file as vcf<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:18 - Read 173 variants into buffer<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:18 - Reading transcript data from cache and/or database<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:19 - Reading regulatory data from cache and/or database<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:19 - Checking for existing variations<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:23 - Analyzing chromosome 21<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:23 - Analyzing variants<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:23 - Analyzing RegulatoryFeatures<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:23 - Analyzing MotifFeatures<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:23 - Calculating consequences<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:24 - Analyzing chromosome 22<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:24 - Analyzing variants<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:24 - Analyzing RegulatoryFeatures<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:24 - Analyzing MotifFeatures<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>2012-11-09 14:01:24 - Calculating consequences<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Can you tell me what might be wrong?<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Cheers<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'><span style='color:#888888'> <o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#888888'>Duarte Molha</span><span style='color:#888888'><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'><span style='color:#888888'> <o:p></o:p></span></p></div></div><p class=MsoNormal style='mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt'><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></p></div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div></div></body></html>