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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='color:#1F497D'>Apologies...<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Just realized I had to change the Condel config file to add the correct path to condel.dir (first line of the Condel config file) <o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Maybe this could be useful information to other users... <o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Do not forget to update the path on the condel config file within your plugin folder to reflect its location...<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>In my case :<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Edit the file:<o:p></o:p></span></p><p class=MsoNormal style='text-indent:36.0pt'><span style='color:#1F497D'> /ReferenceData/vep_cache/Plugins/config/Condel/config/condel_SP.conf'<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Change the the first line to the condel config folder location:<o:p></o:p></span></p><p class=MsoNormal style='text-indent:36.0pt'><span lang=PT style='color:#1F497D'>condel.dir='/ReferenceData/vep_cache/Plugins/config/Condel' <o:p></o:p></span></p><p class=MsoNormal><span lang=PT style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=PT style='color:#1F497D'>Best regards<o:p></o:p></span></p><p class=MsoNormal><span lang=PT style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=PT style='color:#1F497D'>Duarte<o:p></o:p></span></p><p class=MsoNormal><span lang=PT style='color:#1F497D'><o:p> </o:p></span></p><div><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>Duarte Molha<br><b>Sent:</b> 10 May 2012 14:45<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> [ensembl-dev] CONDEL plugin bug?<o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Dear developers<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>I have downloaded the latest VEP and tried to run the example file though it using the condel script and I am getting some error messages:<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Here is the Error output:<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'><u>Command Used:<o:p></o:p></u></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>perl variant_effect_predictor.pl -i example.vcf --dir /ReferenceData/vep_cache/ --plugin Condel,/ReferenceData/vep_cache/Plugins/config/Condel/config,b --force --sift b --polyphen b –verbose<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'><u>OUTPUT:<o:p></o:p></u></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>#----------------------------------#<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'># ENSEMBL VARIANT EFFECT PREDICTOR #<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>#----------------------------------#<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>version 2.5<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>By Will McLaren (<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>)<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Configuration options:<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>core_type core<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>dir /ReferenceData/vep_cache/<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>force_overwrite 1<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>host ensembldb.ensembl.org<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>input_file example.vcf<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>plugin Condel,/ReferenceData/vep_cache/Plugins/config/Condel/config,b<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>polyphen b<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>port 5306<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>sift b<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>species homo_sapiens<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><span lang=PT>toplevel_dir /ReferenceData/vep_cache/<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'>verbose 1<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>--------------------<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Will only load v67 databases<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Species 'homo_sapiens' loaded from database 'homo_sapiens_core_67_37'<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_67_37'<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_67_37'<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_67_37'<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_67_37'<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>homo_sapiens_variation_67_37 loaded<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>homo_sapiens_funcgen_67_37 loaded<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Bio::EnsEMBL::Compara::DBSQL::DBAdaptor not found so the following compara databases will be ignored: ensembl_compara_67<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>ensembl_ancestral_67 loaded<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>ensembl_ontology_67 loaded<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>2012-05-10 14:39:32 - Connected to core version 67 database and variation version 67 database<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>readline() on closed filehandle SIFT at /ReferenceData/vep_cache//Plugins/Condel.pm line 136.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>readline() on closed filehandle POLYPHEN at /ReferenceData/vep_cache//Plugins/Condel.pm line 147.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>2012-05-10 14:39:32 - Loaded plugin: Condel<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>2012-05-10 14:39:33 - Starting...<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>2012-05-10 14:39:33 - Detected format of input file as vcf<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>2012-05-10 14:39:33 - Read 173 variants into buffer<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>2012-05-10 14:39:33 - Analyzing chromosome 21<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>2012-05-10 14:39:33 - Reading transcript data from cache and/or database<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>2012-05-10 14:40:02 - Retrieved 132 transcripts (0 mem, 0 cached, 217 DB, 85 duplicates)<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>2012-05-10 14:40:02 - Analyzing variants<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>2012-05-10 14:40:40 - Calculating and writing output<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>[> ] [ 0% ]Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 203, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>[=============================> ] [ 18% ]Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 203, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 212, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 203, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 212, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 203, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 212, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>[=================================> ] [ 21% ]Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>[==========================================> ] [ 27% ]Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 207, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Use of uninitialized value in subtraction (-) at /ReferenceData/vep_cache//Plugins/Condel.pm line 216, <GEN0> line 175.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>[===============================================> <o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>....<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Can you tell be it there is something wrong with my command line arguments? Or I should just ignore these warining messages?<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Best regards <o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Duarte Molha<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><br><span style='font-family:"Arial","sans-serif"'>Computational Biologist<br>Oxford Gene Technology<br>Begbroke Science Park<br>Sandy Lane Yarnton<br>Oxford OX5 1PF UK</span><span style='font-size:12.0pt;font-family:"Arial","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'><br></span><span lang=FR style='font-size:9.0pt;font-family:"Arial","sans-serif"'>T: +44 (0)1865 856 837</span><span lang=FR style='font-family:"Times New Roman","serif"'><o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span lang=FR style='font-size:9.0pt;font-family:"Arial","sans-serif"'>F: +44 (0)1865 842 116<br>C: +44 (0)7772 111 304<br>E: </span><a href="mailto:duarte.molha@ogt.co.uk"><span lang=FR style='font-size:9.0pt;font-family:"Arial","sans-serif"'>duarte.molha@ogt.co.uk</span></a><span lang=FR style='font-size:9.0pt;font-family:"Arial","sans-serif"'><br>W: </span><a href="http://www.ogt.co.uk/"><span lang=FR style='font-size:9.0pt;font-family:"Arial","sans-serif"'>www.ogt.co.uk</span></a><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'> </span><span lang=FR style='font-size:9.0pt;font-family:"Arial","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span lang=PT><o:p> </o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><b><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#2F3F91'>The complete oligonucleotide array solution for cytogenetics</span></b><b><span lang=EN-US style='color:#2F3F91'><o:p></o:p></span></b></p><p class=MsoNormal style='margin-left:36.0pt;line-height:50%'><b><span lang=EN-US style='font-size:10.0pt;line-height:50%;font-family:"Arial","sans-serif";color:#2F3F91'><o:p> </o:p></span></b></p><p class=MsoNormal style='margin-left:72.0pt;text-indent:-18.0pt;mso-list:l1 level1 lfo3'><![if !supportLists]><span style='font-size:10.0pt;font-family:Symbol;color:#2F3F91'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span lang=EN style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#2F3F91'>Discover how <a href="http://www.ogt.co.uk/cytosure.asp?signature" title="http://www.ogt.co.uk/cytosure.asp?signature"><span style='color:#2F3F91'>CytoSure™ Interpret Software</span></a> can transform your cytogenetics research</span><span lang=EN style='color:#2F3F91'> </span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:#2F3F91'><o:p></o:p></span></p><p class=MsoNormal style='margin-left:72.0pt;text-indent:-18.0pt;mso-list:l1 level1 lfo3'><![if !supportLists]><span style='font-size:10.0pt;font-family:Symbol;color:#2F3F91'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#2F3F91'><a href="http://www.ogt.co.uk/documents/Webselectionguide2.pdf?signature" title="http://www.ogt.co.uk/documents/Webselectionguide2.pdf?signature"><span style='color:#2F3F91'>Select the ideal array for your requirements</span></a> — including our new ISCA designs</span><span lang=EN-US style='color:#2F3F91'> </span><span style='color:#2F3F91'><o:p></o:p></span></p><p class=MsoNormal style='margin-left:72.0pt;text-indent:-18.0pt;mso-list:l1 level1 lfo3'><![if !supportLists]><span style='font-size:10.0pt;font-family:Symbol;color:#2F3F91'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#2F3F91'><a href="http://www.ogt.co.uk/cytosure.asp?signature" title="http://www.ogt.co.uk/cytosure.asp?signature"><span style='color:#2F3F91'>View our complete portfolio</span></a> from DNA labeling and arrays to analysis software and full automation</span><span lang=EN-US style='color:#2F3F91'> </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#2F3F91'><o:p></o:p></span></p><p class=MsoNormal style='margin-left:72.0pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#2F3F91'><o:p> </o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><b><span lang=EN style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#2F3F91'>Discover the power of CytoSure products and get your chance to <a href="http://www.ogt.co.uk/cytosure.asp?signature" title="http://www.ogt.co.uk/cytosure.asp?signature"><span style='color:#2F3F91'>win one of three iPod Nanos</span></a>!<o:p></o:p></span></b></p><p class=MsoNormal style='margin-left:36.0pt'><b><span lang=EN style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#2F3F91'><o:p> </o:p></span></b></p><p class=MsoNormal style='mso-margin-top-alt:auto;margin-left:36.0pt'><b><span lang=EN style='font-size:7.5pt;font-family:"Arial","sans-serif";color:#002060'>CytoSure™</span></b><span lang=EN style='font-size:7.5pt;font-family:"Arial","sans-serif";color:#002060'>: For research use only<br></span><span lang=EN-US style='font-size:7.5pt;font-family:"Arial","sans-serif";color:navy'>This product is provided under an agreement between Agilent Technologies, Inc. and OGT. The manufacture, use, sale or import of this products may be subject to one or more of U.S. patents, pending applications, and corresponding international equivalents, owned by Agilent Technologies, Inc. The purchaser has the non-transferable right to use and consume the product for RESEARCH USE ONLY AND NOT for DIAGNOSTICS PROCEDURES. It is not intended for use, and should not be used for the diagnosis, prevention, monitoring, treatment or alleviation of any disease or condition, or for the investigation of any physiological process, in any identifiable human, or for any other medical purpose.</span><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div></body></html>