<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 12 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:583879744;
mso-list-template-ids:-658741542;}
@list l0:level1
{mso-level-number-format:bullet;
mso-level-text:\F0B7;
mso-level-tab-stop:36.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Symbol;}
@list l0:level2
{mso-level-tab-stop:72.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level3
{mso-level-tab-stop:108.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level4
{mso-level-tab-stop:144.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level5
{mso-level-tab-stop:180.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level6
{mso-level-tab-stop:216.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level7
{mso-level-tab-stop:252.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level8
{mso-level-tab-stop:288.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level9
{mso-level-tab-stop:324.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</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>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><o:p> </o:p></p><p class=MsoNormal>Here is the Error output:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><u>Command Used:<o:p></o:p></u></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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><o:p> </o:p></p><p class=MsoNormal><u>OUTPUT:<o:p></o:p></u></p><p class=MsoNormal><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 2.5<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>core_type core<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>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>sift b<o:p></o:p></p><p class=MsoNormal>species homo_sapiens<o:p></o:p></p><p class=MsoNormal><span lang=PT>toplevel_dir /ReferenceData/vep_cache/<o:p></o:p></span></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 v67 databases<o:p></o:p></p><p class=MsoNormal>Species 'homo_sapiens' loaded from database 'homo_sapiens_core_67_37'<o:p></o:p></p><p class=MsoNormal>Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_67_37'<o:p></o:p></p><p class=MsoNormal>Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_67_37'<o:p></o:p></p><p class=MsoNormal>Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_67_37'<o:p></o:p></p><p class=MsoNormal>Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_67_37'<o:p></o:p></p><p class=MsoNormal>homo_sapiens_variation_67_37 loaded<o:p></o:p></p><p class=MsoNormal>homo_sapiens_funcgen_67_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_67<o:p></o:p></p><p class=MsoNormal>ensembl_ancestral_67 loaded<o:p></o:p></p><p class=MsoNormal>ensembl_ontology_67 loaded<o:p></o:p></p><p class=MsoNormal>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>readline() on closed filehandle SIFT at /ReferenceData/vep_cache//Plugins/Condel.pm line 136.<o:p></o:p></p><p class=MsoNormal>readline() on closed filehandle POLYPHEN at /ReferenceData/vep_cache//Plugins/Condel.pm line 147.<o:p></o:p></p><p class=MsoNormal>2012-05-10 14:39:32 - Loaded plugin: Condel<o:p></o:p></p><p class=MsoNormal>2012-05-10 14:39:33 - Starting...<o:p></o:p></p><p class=MsoNormal>2012-05-10 14:39:33 - Detected format of input file as vcf<o:p></o:p></p><p class=MsoNormal>2012-05-10 14:39:33 - Read 173 variants into buffer<o:p></o:p></p><p class=MsoNormal>2012-05-10 14:39:33 - Analyzing chromosome 21<o:p></o:p></p><p class=MsoNormal>2012-05-10 14:39:33 - 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>2012-05-10 14:40:02 - Retrieved 132 transcripts (0 mem, 0 cached, 217 DB, 85 duplicates)<o:p></o:p></p><p class=MsoNormal>2012-05-10 14:40:02 - Analyzing variants<o:p></o:p></p><p class=MsoNormal>[====================================================================================================================================================================] [ 100% ]<o:p></o:p></p><p class=MsoNormal>2012-05-10 14:40:40 - Calculating and writing output<o:p></o:p></p><p class=MsoNormal>[> ] [ 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>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>[=============================> ] [ 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>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>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>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>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>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>[=================================> ] [ 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>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>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>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>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>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>[==========================================> ] [ 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>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>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>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>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>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>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>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>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>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>[===============================================> <o:p></o:p></p><p class=MsoNormal>....<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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><o:p> </o:p></p><p class=MsoNormal>Best regards <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<o:p></o:p></span></p><p class=MsoNormal><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><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><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";color:blue'>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";color:blue'>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><span lang=PT><o:p> </o:p></span></p><p class=MsoNormal><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='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><ul style='margin-top:0cm' type=disc><li class=MsoNormal style='color:#2F3F91;mso-list:l0 level1 lfo1'><span lang=EN style='font-size:10.0pt;font-family:"Arial","sans-serif"'>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> </span><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></li><li class=MsoNormal style='color:#2F3F91;mso-list:l0 level1 lfo1'><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif"'><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> </span><o:p></o:p></li><li class=MsoNormal style='color:#2F3F91;mso-list:l0 level1 lfo1'><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif"'><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> </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p></o:p></span></li></ul><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#2F3F91'><o:p> </o:p></span></p><p class=MsoNormal><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><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'><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><o:p> </o:p></p></div></body></html>