<html><head><base href="x-msg://215/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Duarte<div><br></div><div>That is caused by a bad logical test which I have corrected in the patch below(updated on the head). However, this is indicative of another problem as the reason it is dying is due to the Slice argument being passed to the method in question, being undefined.</div><div><br></div><div>...over to Will</div><div><br></div><div>Thanks</div><div><br></div><div>Nath</div><div><br></div><div><br></div><div><div>Index: BaseFeatureAdaptor.pm</div><div>===================================================================</div><div>RCS file: /nfs/ensembl/cvsroot/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/BaseFeatureAdaptor.pm,v</div><div>retrieving revision 1.65</div><div>diff -u -r1.65 BaseFeatureAdaptor.pm</div><div>--- BaseFeatureAdaptor.pm 16 Jul 2012 12:10:40 -0000 1.65</div><div>+++ BaseFeatureAdaptor.pm 14 Sep 2012 11:52:48 -0000</div><div>@@ -5,7 +5,7 @@</div><div> </div><div> =head1 LICENSE</div><div> </div><div>- Copyright (c) 1999-2011 The European Bioinformatics Institute and</div><div>+ Copyright (c) 1999-2012 The European Bioinformatics Institute and</div><div> Genome Research Limited. All rights reserved.</div><div> </div><div> This software is distributed under a modified Apache license.</div><div>@@ -132,8 +132,8 @@</div><div> </div><div> my @result;</div><div> </div><div>- if(!ref($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {</div><div>- throw("Bio::EnsEMBL::Slice argument expected.");</div><div>+ if(! (ref($slice) && $slice->isa('Bio::EnsEMBL::Slice')) {</div><div>+ throw('Bio::EnsEMBL::Slice argument expected.');</div><div> }</div><div> </div><div> $constraint ||= '';</div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br><div><div>On 14 Sep 2012, at 12:44, Duarte Molha wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Dear developers,<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">I am sorry to bother you again (especially Will<span class="Apple-converted-space"> </span><span style="font-family: Wingdings; ">J</span><span class="Apple-converted-space"> </span>) but in testing the VEP26, I got a crash using the command:<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">perl variant_effect_predictor.pl -i input_variants.vcf.gz -o output.ann --config vep.ini<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Here is the error output:<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">2012-09-14 12:29:30 - Reading regulatory data from cache and/or database<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">[==================================> ] [ 22% ]<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Can't call method "isa" on unblessed reference at /NGS_Tools/bin/VEP_26_testing/Bio/EnsEMBL/Funcgen/DBSQL/BaseFeatureAdaptor.pm line 135, <GEN0> line 28406.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">In attachment is the config file I use.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Best regards,<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: 36pt; "><span style="font-size: 10pt; font-family: Arial, sans-serif; ">Duarte Molha</span><span style="font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div><span><vep.ini></span>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" style="color: blue; text-decoration: underline; ">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe):<span class="Apple-converted-space"> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev" style="color: blue; text-decoration: underline; ">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog:<span class="Apple-converted-space"> </span><a href="http://www.ensembl.info/" style="color: blue; text-decoration: underline; ">http://www.ensembl.info/</a><br></div></blockquote></div><br><div>
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