<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Johannes<div>I am glad that the workaround is okay but please let me know if you would like me to generate the results for you and I will do so. </div><div>Regards</div><div>Rhoda</div><div><br></div><div><br><div><div>On 7 Oct 2011, at 16:19, Johannes Meisig wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Rhoda,<br><br>thanks for answering so quickly! As a workaround, I make the database query the other way around. It's a bit slower because I have to plug in the whole genome now, but that's not a big problem.<br><br>Johannes<br><br>Rhoda Kinsella wrote:<br><blockquote type="cite">Hi Johannes<br></blockquote><blockquote type="cite">This is a known bug (please see here: <a href="http://www.ensembl.info/contact-us/known-bugs/)">http://www.ensembl.info/contact-us/known-bugs/)</a>. This known bugs page includes a temporary workaround. Unfortunately we will not be able to make the bug fix live until our next release 65 due out in November. I have, however, fixed this on an internal server and am happy to run your query for you if you send me your list of query RefSeq IDs. I hope that helps,<br></blockquote><blockquote type="cite">Regards<br></blockquote><blockquote type="cite">Rhoda<br></blockquote><blockquote type="cite"> On 6 Oct 2011, at 15:16, Johannes Meisig wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite">Hi,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">a month I started using Ensembl/Biomart to find Ensembl Gene IDs<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">corresponding to Refseq IDs. When I tried it again yesterday it didn't<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">work anymore.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Selecting Ensembl Gene ID and Ensembl Transcript ID as attributes and<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Refseq mRNA ID with the Mus musculus genes dataset I get the error<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">attached to this message on the website.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">The error can be easily reproduced by plugging in the example ID<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">NM_01195597 into the ID list. Is this problem known? Is there anything I<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">should do differently?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Johannes<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Serious Error: Error during query execution: Table<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ERROR: caught BioMart::Exception::Database: Error during query<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">execution: Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">If you repeatedly get directed to this error page, there may be a<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">problem with your current session parameters. To clear your session and<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">start with a clean slate, please click the New button below.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Stacktrace:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Exception::Class::Base::throw<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Dataset/TableSet.pm:241<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">BioMart::Dataset::TableSet::_fillAttributeTableWith<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">BioMart::Dataset::TableSet::_getResultTable<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/DatasetI.pm:1170<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">BioMart::DatasetI::getResultTable<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/QueryRunner.pm:472<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">BioMart::QueryRunner::_processPath<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/QueryRunner.pm:374<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">BioMart::QueryRunner::_getResultTable<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/QueryRunner.pm:194<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">BioMart::QueryRunner::execute<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Web.pm:2464<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">(eval) /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Web.pm:2216<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">BioMart::Web::handle_request<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/ensemblweb/wwwmart/www_64/biomart-perl/cgi-bin/martview:100<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">(eval) /ensemblweb/wwwmart/www_64/biomart-perl/cgi-bin/martview:99<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ModPerl::ROOT::ModPerl::Registry::ensemblweb_wwwmart_www_64_biomart_2dperl_cgi_2dbin_martview::handler <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">(eval)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ModPerl::RegistryCooker::run<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ModPerl::RegistryCooker::default_handler<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">/localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/Registry.pm:31<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ModPerl::Registry::handler -e:0<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">(eval) -e:0<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Dev mailing list Dev@ensembl.org <<a href="mailto:Dev@ensembl.org">mailto:Dev@ensembl.org</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote></blockquote><blockquote type="cite">Rhoda Kinsella Ph.D.<br></blockquote><blockquote type="cite">Ensembl Production Project Leader,<br></blockquote><blockquote type="cite">European Bioinformatics Institute (EMBL-EBI),<br></blockquote><blockquote type="cite">Wellcome Trust Genome Campus, Hinxton<br></blockquote><blockquote type="cite">Cambridge CB10 1SD,<br></blockquote><blockquote type="cite">UK.<br></blockquote></div></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; 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; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; 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; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Rhoda Kinsella Ph.D.</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Ensembl Production Project Leader,</div></div><div>European Bioinformatics Institute (EMBL-EBI),<br>Wellcome Trust Genome Campus, </div><div>Hinxton<br>Cambridge CB10 1SD,</div><div>UK.</div></div></span></div></span></div></span> </div><br></div></body></html>