<div>Ah, great thanks!</div>
<div class="mailbox_signature">
<br>-Konrad</div>
<br><br><div class="gmail_quote"><p>On Fri, May 29, 2015 at 4:19 AM, njohnson <span dir="ltr"><<a href="mailto:njohnson@ebi.ac.uk" target="_blank">njohnson@ebi.ac.uk</a>></span> wrote:<br></p><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><p>Hi Konrad
<br><br>I am assuming you are still using v79? In version 80 we put in a stop gap solution to ignore these motifs, so the VEP should not longer die in these cases. We hope to put in a more robust solution once we have decided on the best approach.
<br><br>Thanks
<br><br>Nathan Johnson
<br><br>Ensembl Regulation
<br>European Bioinformatics Institute (EMBL-EBI)
<br>European Molecular Biology Laboratory
<br>Wellcome Trust Genome Campus
<br>Hinxton
<br>Cambridge CB10 1SD
<br>United Kingdom
<br><br>http://www.ensembl.info/
<br>http://twitter.com/#!/ensembl
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<br><br>> On 29 May 2015, at 09:08, Daniel Zerbino <zerbino@ebi.ac.uk> wrote:
<br>>
<br>> Hello Konrad,
<br>>
<br>> Thanks, we're working on it now.
<br>>
<br>> Cheers,
<br>>
<br>> Daniel
<br>>
<br>> On 5/29/15 5:36 AM, Konrad Karczewski wrote:
<br>>> Hi Ensembl/VEP team,
<br>>>
<br>>> Another corner case variant (yay!), though this one doesn't look as bad (or at least is obvious what's going on). Found the following variant (don't ask how):
<br>>>
<br>>> 2 92326168 . G T
<br>>>
<br>>> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&highlight=hg19.chr2%3A92326168-92326168&position=chr2%3A92326123-92326212
<br>>>
<br>>> that happens to sit near a bunch of N's in the reference genome, which is throwing an error (I'm guessing in looking for motifs) as shown below.
<br>>>
<br>>> -Konrad
<br>>>
<br>>> -------------------- EXCEPTION --------------------
<br>>> MSG: Sequence GCTTNNNNNNNNNNNNN contains invalid characters: Only Aa Cc Gg Tt accepted
<br>>> STACK Bio::EnsEMBL::Funcgen::BindingMatrix::relative_affinity /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Funcgen/BindingMatrix.pm:301
<br>>> STACK Bio::EnsEMBL::Variation::MotifFeatureVariationAllele::motif_score_delta /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/MotifFeatureVariationAllele.pm:226
<br>>> STACK Bio::EnsEMBL::Variation::Utils::VEP::mfva_to_line /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:2371
<br>>> STACK Bio::EnsEMBL::Variation::Utils::VEP::vfoa_to_line /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:2130
<br>>> STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_to_consequences /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1844
<br>>> STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_list_to_cons /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1373
<br>>> STACK Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1202
<br>>> STACK main::main /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/variant_effect_predictor.pl:313
<br>>> STACK toplevel /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/variant_effect_predictor.pl:144
<br>>> Date (localtime) = Wed May 27 18:28:55 2015
<br>>> Ensembl API version = 79
<br>>>
<br>>>
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<br></p></blockquote></div><br>