Hi Stephen, This is a known bug in BioMart release 64 : http://www.ensembl.info/contact-us/known-bugs/
This bug will be fixed for release 65 due out in November. If your query is urgent you can send me your list of IDs and I can get the results for you. Apologies for the inconvenience caused, Best Regards, Thomas On 26 Oct 2011, at 22:35, Arek Kasprzyk wrote: > Hi Stephen, > It seems like Ensembl mart maybe misconfigured. I am cc'ing your email to the > users mailing list so someone from Ensembl will be able to help you > > a > > On Wed, Oct 26, 2011 at 5:24 PM, Turner, Stephen (sdt5z) <[email protected]> > wrote: > Arek, > > > > Not sure who I should be sending this to. I was trying to use Biomart to > convert RefSeq transcript IDs to ensembl gene ids / names, and I have this > error whenever I filter results using RefSeq mRNA ids. It looks like it isn’t > able to query the ensembl to refseq table or something. Let me know who I > should contact about this. > > > > Thakns, > > > > Stephen > > > > > > View rows as Unique results only > > Serious Error: Error during query execution: Table > 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist > > > > ERROR: caught BioMart::Exception::Database: Error during query execution: > Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist > > > > If you repeatedly get directed to this error page, there may be a problem > with your current session parameters. To clear your session and start with a > clean slate, please click the New button below. > > > > Stacktrace: > > Exception::Class::Base::throw > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/TableSet.pm:241 > > BioMart::Dataset::TableSet::_fillAttributeTableWith > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124 > > BioMart::Dataset::TableSet::_getResultTable > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/DatasetI.pm:1170 > > BioMart::DatasetI::getResultTable > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:472 > > BioMart::QueryRunner::_processPath > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:374 > > BioMart::QueryRunner::_getResultTable > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:194 > > BioMart::QueryRunner::execute > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2433 > > (eval) /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2201 > > BioMart::Web::handle_request > /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:96 > > (eval) /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:95 > > ModPerl::ROOT::ModPerl::Registry::srv_biomart_server_biomart_2eorg_biomart_2dperl_cgi_2dbin_martview::handler > /usr/lib/perl5/ModPerl/RegistryCooker.pm:204 > > (eval) /usr/lib/perl5/ModPerl/RegistryCooker.pm:204 > > ModPerl::RegistryCooker::run /usr/lib/perl5/ModPerl/RegistryCooker.pm:170 > > ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/Registry.pm:31 > > ModPerl::Registry::handler -e:0 > > (eval) -e:0 > > > > ---------------------------------- > > Stephen Turner, Ph.D. > > Bioinformatics Core Director > > Department of Public Health Sciences > > University of Virginia School of Medicine > > > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge - CB10 1SD - UK
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