<div>Hi Duarte,</div><div><br></div>--debug (debug => 1 in your config) is not for external use<div><br></div><div>Will</div><div class="gmail_extra"><br><br><div class="gmail_quote">On 9 November 2012 14:02, Duarte Molha <span dir="ltr"><<a href="mailto:Duarte.Molha@ogt.co.uk" target="_blank">Duarte.Molha@ogt.co.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-GB" link="blue" vlink="purple"><div><p class="MsoNormal">Dear Developers<u></u><u></u></p><p class="MsoNormal">
<u></u> <u></u></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.<u></u><u></u></p><p class="MsoNormal">
<u></u> <u></u></p><p class="MsoNormal">Here is the output:<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --config vep_custom.ini -i example.vcf --debug<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:17 - Read configuration from vep_custom.ini<u></u><u></u></p><p class="MsoNormal">#----------------------------------#<u></u><u></u></p><p class="MsoNormal"># ENSEMBL VARIANT EFFECT PREDICTOR #<u></u><u></u></p>
<p class="MsoNormal">#----------------------------------#<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">version 2.7<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">
By Will McLaren (<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Configuration options:<u></u><u></u></p><p class="MsoNormal">
<u></u> <u></u></p><p class="MsoNormal">buffer_size 50000<u></u><u></u></p><p class="MsoNormal">cache 1<u></u><u></u></p><p class="MsoNormal">check_existing 1<u></u><u></u></p><p class="MsoNormal">
config vep_custom.ini<u></u><u></u></p><p class="MsoNormal">core_type core<u></u><u></u></p><p class="MsoNormal">debug 1<u></u><u></u></p><p class="MsoNormal">dir /ReferenceData/vep_cache/<u></u><u></u></p>
<p class="MsoNormal">force_overwrite 1<u></u><u></u></p><p class="MsoNormal">gmaf 1<u></u><u></u></p><p class="MsoNormal">host <a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a><u></u><u></u></p>
<p class="MsoNormal">input_file example.vcf<u></u><u></u></p><p class="MsoNormal">plugin Condel,/ReferenceData/vep_cache/Plugins/config/Condel/config,b<u></u><u></u></p><p class="MsoNormal">polyphen b<u></u><u></u></p>
<p class="MsoNormal">port 5306<u></u><u></u></p><p class="MsoNormal">protein 1<u></u><u></u></p><p class="MsoNormal">regulatory 1<u></u><u></u></p><p class="MsoNormal">sift b<u></u><u></u></p>
<p class="MsoNormal">species homo_sapiens<u></u><u></u></p><p class="MsoNormal">terms display<u></u><u></u></p><p class="MsoNormal">toplevel_dir /ReferenceData/vep_cache/<u></u><u></u></p><p class="MsoNormal">
verbose 1<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">--------------------<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Will only load v69 databases<u></u><u></u></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from database 'homo_sapiens_core_69_37'<u></u><u></u></p><p class="MsoNormal">Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_69_37'<u></u><u></u></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_69_37'<u></u><u></u></p><p class="MsoNormal">Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_69_37'<u></u><u></u></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_69_37'<u></u><u></u></p><p class="MsoNormal">homo_sapiens_variation_69_37 loaded<u></u><u></u></p><p class="MsoNormal">
homo_sapiens_funcgen_69_37 loaded<u></u><u></u></p><p class="MsoNormal">Bio::EnsEMBL::Compara::DBSQL::DBAdaptor not found so the following compara databases will be ignored: ensembl_compara_69<u></u><u></u></p><p class="MsoNormal">
ensembl_ancestral_69 loaded<u></u><u></u></p><p class="MsoNormal">ensembl_ontology_69 loaded<u></u><u></u></p><p class="MsoNormal">2012-11-09 14:01:18 - Connected to core version 69 database and variation version 69 database<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:18 - Read existing cache info<u></u><u></u></p><p class="MsoNormal">2012-11-09 14:01:18 - Loaded plugin: Condel<u></u><u></u></p><p class="MsoNormal">2012-11-09 14:01:18 - Starting...<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:18 - Detected format of input file as vcf<u></u><u></u></p><p class="MsoNormal">2012-11-09 14:01:18 - Read 173 variants into buffer<u></u><u></u></p><p class="MsoNormal">2012-11-09 14:01:18 - Reading transcript data from cache and/or database<u></u><u></u></p>
<p class="MsoNormal">[====================================================================================================================================================================] [ 100% ]<u></u><u></u></p><p class="MsoNormal">
2012-11-09 14:01:19 - Retrieved 3090 transcripts (0 mem, 3176 cached, 0 DB, 86 duplicates)<u></u><u></u></p><p class="MsoNormal">2012-11-09 14:01:19 - Reading regulatory data from cache and/or database<u></u><u></u></p><p class="MsoNormal">
[====================================================================================================================================================================] [ 100% ]<u></u><u></u></p><p class="MsoNormal">2012-11-09 14:01:19 - Retrieved 13706 regulatory features (0 mem, 13710 cached, 0 DB, 4 duplicates)<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:19 - Checking for existing variations<u></u><u></u></p><p class="MsoNormal">[====================================================================================================================================================================] [ 100% ]<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:23 - Analyzing chromosome 21<u></u><u></u></p><p class="MsoNormal">2012-11-09 14:01:23 - Analyzing variants<u></u><u></u></p><p class="MsoNormal">[====================================================================================================================================================================] [ 100% ]<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:23 - Analyzing RegulatoryFeatures<u></u><u></u></p><p class="MsoNormal">[====================================================================================================================================================================] [ 100% ]<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:23 - Analyzing MotifFeatures<u></u><u></u></p><p class="MsoNormal">[====================================================================================================================================================================] [ 100% ]<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:23 - Calculating consequences<u></u><u></u></p><p class="MsoNormal">[====================================================================================================================================================================] [ 100% ]<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:24 - Analyzing chromosome 22<u></u><u></u></p><p class="MsoNormal">2012-11-09 14:01:24 - Analyzing variants<u></u><u></u></p><p class="MsoNormal">[====================================================================================================================================================================] [ 100% ]<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:24 - Analyzing RegulatoryFeatures<u></u><u></u></p><p class="MsoNormal">[====================================================================================================================================================================] [ 100% ]<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:24 - Analyzing MotifFeatures<u></u><u></u></p><p class="MsoNormal">[====================================================================================================================================================================] [ 100% ]<u></u><u></u></p>
<p class="MsoNormal">2012-11-09 14:01:24 - Calculating consequences<u></u><u></u></p><p class="MsoNormal">[====================================================================================================================================================================] [ 100% ]<u></u><u></u></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.<u></u><u></u></p><p class="MsoNormal">
<u></u> <u></u></p><p class="MsoNormal">Can you tell me what might be wrong?<u></u><u></u></p><p class="MsoNormal">Cheers<span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></p><span class="HOEnZb"><font color="#888888"><p class="MsoNormal">
<u></u> <u></u></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""><u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p></font></span></div></div><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><br>
<br></blockquote></div><br></div>