<div dir="ltr">Hi Stefan,<div><br></div><div>The 79 databases were only brought online to <a href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a> earlier today; this was probably the cause of your error, but it should work OK now.</div><div><br></div><div>We are also experiencing delays getting our FTP site up, which carries the VEP 79 cache files; we hope to make this available soon.</div><div><br></div><div>Thanks for your patience</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 13 March 2015 at 16:24, Stefan Gräf <span dir="ltr"><<a href="mailto:sg550@cam.ac.uk" target="_blank">sg550@cam.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Will,<div><br></div><div>Looks like this bug sneaked in again with v79:</div><div><br></div><div>All best,</div><div> Stefan</div><div><br></div><div><div><font face="monospace, monospace">-------------------- WARNING ----------------------</font></div><div><font face="monospace, monospace">MSG: homo_sapiens is not a valid species name (check DB and API version)</font></div><div><font face="monospace, monospace">FILE: Bio/EnsEMBL/Registry.pm LINE: 1200</font></div><div><font face="monospace, monospace">CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 985</font></div><div><font face="monospace, monospace">Date (localtime)    = Fri Mar 13 16:13:37 2015</font></div><div><font face="monospace, monospace">Ensembl API version = 79</font></div><div><font face="monospace, monospace">---------------------------------------------------</font></div><span class=""><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">-------------------- EXCEPTION --------------------</font></div><div><font face="monospace, monospace">MSG: Can not find internal name for species 'homo_sapiens'</font></div></span><div><font face="monospace, monospace">STACK Bio::EnsEMBL::Registry::get_adaptor /home/cbrcmod/scratch/modules/out/modulebin/VEP/79/perl/Bio/EnsEMBL/Registry.pm:987</font></div><div><font face="monospace, monospace">STACK main::connect_to_dbs /home/cbrcmod/scratch/modules/out/modulebin/VEP/79/bin/<a href="http://variant_effect_predictor.pl:1191" target="_blank">variant_effect_predictor.pl:1191</a></font></div><div><font face="monospace, monospace">STACK main::configure /home/cbrcmod/scratch/modules/out/modulebin/VEP/79/bin/<a href="http://variant_effect_predictor.pl:780" target="_blank">variant_effect_predictor.pl:780</a></font></div><div><font face="monospace, monospace">STACK toplevel /home/cbrcmod/scratch/modules/out/modulebin/VEP/79/bin/<a href="http://variant_effect_predictor.pl:141" target="_blank">variant_effect_predictor.pl:141</a></font></div><div><font face="monospace, monospace">Date (localtime)    = Fri Mar 13 16:13:37 2015</font></div><div><font face="monospace, monospace">Ensembl API version = 79</font></div><div><font face="monospace, monospace">---------------------------------------------------</font></div></div><div><br></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On 4 December 2014 at 10:51, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Konrad,<div><br></div><div>Thanks for finding this, I've pushed a fix to 77 and 78 (ensembl-variation).</div><div><br></div><div>In general though, I would advise against mixing different software and cache releases if you can avoid it.</div><div><br></div><div>Cheers</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On 4 December 2014 at 01:18, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div style="word-wrap:break-word">Hi VEP crew,<div><br></div><div>I've been trying to use newer versions of VEP (77/78) with older versions of the cache (74) and seem to be running into some issues (stack trace below). Any ideas?</div><div><br></div><div>Thanks!</div><div>-Konrad</div><div><br></div><div><div>-------------------- EXCEPTION --------------------</div><div>MSG: Can not find internal name for species 'homo_sapiens'</div><div>STACK Bio::EnsEMBL::Registry::get_adaptor /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Registry.pm:987</div><div>STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:1016</div><div>STACK Bio::EnsEMBL::Translation::get_all_Attributes /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Translation.pm:995</div><div>STACK Bio::EnsEMBL::Translation::get_all_SeqEdits /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Translation.pm:1069</div><div>STACK Bio::EnsEMBL::Variation::BaseTranscriptVariation::_selenocysteine_positions /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/BaseTranscriptVariation.pm:733</div><div>STACK Bio::EnsEMBL::Variation::TranscriptVariationAllele::peptide /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm:248</div><div>STACK Bio::EnsEMBL::Variation::TranscriptVariation::pep_allele_string /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariation.pm:230</div><div>STACK Bio::EnsEMBL::Variation::TranscriptVariation::_prefetch_for_vep /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariation.pm:436</div><div>STACK Bio::EnsEMBL::Variation::Utils::VEP::whole_genome_fetch_transcript /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:3143</div><div>STACK Bio::EnsEMBL::Variation::Utils::VEP::whole_genome_fetch /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:2997</div><div>STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_list_to_cons /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1387</div><div>STACK Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1271</div><div>STACK main::main /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl:280" target="_blank">variant_effect_predictor.pl:280</a></div><div>STACK toplevel /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl:144" target="_blank">variant_effect_predictor.pl:144</a></div><div>Date (localtime)    = Wed Dec  3 20:13:21 2014</div><div>Ensembl API version = 77</div><div>---------------------------------------------------</div></div><div><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br></div></div></div></div></div><br></div></div>_______________________________________________<br>
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