<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Variant Effect Predictor error: Can't call method "description" on an undefined value at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 910, <GEN1> line 205.</div></div><div><br></div><div>VEP 2.3</div><div>local copy of database v 65</div><div><br></div><div>input VCF:</div><div><div>$vf->{_line} = </div><div>1<span class="Apple-tab-span" style="white-space: pre; "> </span>226497256<span class="Apple-tab-span" style="white-space: pre; "> </span>TF_binding_site_variant<span class="Apple-tab-span" style="white-space: pre; "> </span>G<span class="Apple-tab-span" style="white-space: pre; "> </span>A<span class="Apple-tab-span" style="white-space: pre; "> </span>.<span class="Apple-tab-span" style="white-space: pre; "> </span>.<span class="Apple-tab-span" style="white-space: pre; "> </span>.</div><div><br></div></div><div>VEP.pm line 910:</div><div><div> my $matrix = $mf->binding_matrix->description.' '.$mf->display_label;</div><div><br></div><div>$mf = Bio::EnsEMBL::Variation::MotifFeature</div><div>$mf->{binding_matrix} = undef</div><div>$mf->{dbID} = 625091</div><div><div>$mf->{display_label} = Gapb:PB0124.1</div></div><div><div>$mf->{end} = 226497270</div></div><div><div>$mf->{interdb_stable_id} = undef</div></div><div><div>$mf->{score} = 0.898</div></div><div><div>$mf->{slice} = Bio::EnsEMBL::Slice</div></div><div><div><div>$mf->{start} = 226497255</div></div></div><div><div><div>$mf->{strand} = −1</div></div></div><div><div><div><br></div></div></div><div>STDOUT/STDERR:</div><div><div>Use of qw(...) as parentheses is deprecated at /home/myourshaw/lab/pypeline/vax23/vax23.pl line 852.</div><div>2011-12-18 10:35:24 - Reading configuration from /home/myourshaw/lab/pypeline/vax23/vep.ini</div><div>#----------------------------------#</div><div># ENSEMBL VARIANT EFFECT PREDICTOR #</div><div>#----------------------------------#</div><div><br></div><div>version 2.3</div><div><br></div><div>By Will McLaren (<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>)</div><div><br></div><div>Configuration options:</div><div><br></div><div> </div><div>canonical 1</div><div>check_ref 1</div><div>condel b</div><div>config /home/myourshaw/lab/pypeline/vax23/vep.ini</div><div>core_type core</div><div>dir /home/myourshaw/.vep</div><div>force_overwrite 1</div><div>format vcf</div><div>gene 1</div><div>hgnc 1</div><div>hgvs 1</div><div>host cortex.local</div><div>input_file /home/myourshaw/lab/pypeline/vax23/snp_test.vcf</div><div>no_progress 1</div><div>output_file /home/myourshaw/lab/pypeline/vax23/snp_test.vcf.vax</div><div>password ?</div><div>polyphen b</div><div>port 3306</div><div>protein 1</div><div>regulatory 1</div><div>sift b</div><div>species human</div><div>terms SO</div><div>user ?</div><div>verbose 1</div><div><br></div><div>--------------------</div><div><br></div><div>Will only load v65 databases</div><div>Species 'homo_sapiens' loaded from database 'homo_sapiens_core_65_37'</div><div>Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_65_37'</div><div>Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_65_37'</div><div>Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_65_37'</div><div>Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_65_37'</div><div>homo_sapiens_variation_65_37 loaded</div><div>homo_sapiens_funcgen_65_37 loaded</div><div>ensembl_compara_65 loaded</div><div>ensembl_ancestral_65 loaded</div><div>ensembl_ontology_65 loaded</div><div>2011-12-18 10:35:24 - Connected to core version 65 database and variation version 65 database</div><div>2011-12-18 10:35:24 - Starting...</div><div>2011-12-18 10:35:27 - Read 204 variants into buffer</div><div>2011-12-18 10:35:27 - Analyzing chromosome 1</div><div>2011-12-18 10:35:27 - Reading transcript data from cache and/or database</div><div>2011-12-18 10:35:29 - Retrieved 449 transcripts (0 mem, 0 cached, 460 DB, 11 duplicates)</div><div>2011-12-18 10:35:29 - Analyzing variants</div><div>2011-12-18 10:35:36 - Reading regulatory data from cache and/or database</div><div>2011-12-18 10:35:38 - Retrieved 208 regulatory features (0 mem, 0 cached, 208 DB, 0 duplicates)</div><div>2011-12-18 10:35:38 - Analyzing RegulatoryFeatures</div><div>2011-12-18 10:35:38 - Analyzing MotifFeatures</div><div>2011-12-18 10:35:38 - Calculating and writing output</div><div>Can't call method "description" on an undefined value at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 910, <GEN1> line 205.</div></div><div><br></div><div><br></div><div apple-content-edited="true">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-family: Helvetica; font-size: 12px; "><p class="MsoNormal" style="font-family: 'Lucida Grande'; font-size: 10px; "><font class="Apple-style-span" face="'Devanagari MT'" size="7"><span class="Apple-style-span" style="font-size: 27px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br class="Apple-interchange-newline"></span></font></span><span class="Apple-style-span" style="font-size: 27px; "><font class="Apple-style-span" size="5"><span class="Apple-style-span" style="font-size: 18px; ">ॐ</span></font></span></font></p><p></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; line-height: 19px; font: normal normal normal 16px/normal Helvetica; "><span class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: 10px; ">Michael Yourshaw</span></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">UCLA Geffen School of Medicine</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Department of Human Genetics, Nelson Lab</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">695 Charles E Young Drive S</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Gonda 5554</span></div><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Los Angeles CA 90095-8348 USA</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; color: rgb(0, 0, 153); "><span style="text-decoration: underline; letter-spacing: 0px; "><a href="mailto:myourshaw@ucla.edu">myourshaw@ucla.edu</a></span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">970.691.8299</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 9px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this communication in error, please erase all copies of the message and its attachments and notify us immediately. Thank you.</span></p><div><font class="Apple-style-span" size="1"><span class="Apple-style-span" style="font-size: 9px; "><br></span></font></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline"></div>
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