Forward to Ensembl team that is responsible for the Ensembl marts.
Begin forwarded message: From: Gabriel Berriz <gber...@hms.harvard.edu<mailto:gber...@hms.harvard.edu>> Date: September 3, 2010 3:03:27 PM EDT To: "mart-dev@ebi.ac.uk<mailto:mart-dev@ebi.ac.uk>" <mart-dev@ebi.ac.uk<mailto:mart-dev@ebi.ac.uk>> Cc: Kenny Chua <hnc...@i2r.a-star.edu.sg<mailto:hnc...@i2r.a-star.edu.sg>> Subject: [mart-dev] possible biomart bug Hi. The following queries result in the server-side errors shown: <Query completionStamp="1" virtualSchemaName="default" uniqueRows="1" requestId="biomart-client"> <Dataset interface="default" name="dmelanogaster_gene_ensembl"> <Attribute name="merops"/> </Dataset> </Query> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_MEROPS__dm.translation_id_1068_key' in 'where clause' <Query completionStamp="1" virtualSchemaName="default" uniqueRows="1" requestId="biomart-client"> <Dataset interface="default" name="dmelanogaster_gene_ensembl"> <Attribute name="pdb"/> </Dataset> </Query> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_PDB__dm.translation_id_1068_key' in 'where clause' (drosophila_melanogaster/pdb) Other similar queries work fine. E.g.: <Query completionStamp="1" virtualSchemaName="default" uniqueRows="1" requestId="biomart-client"> <Dataset interface="default" name="dmelanogaster_gene_ensembl"> <Attribute name="embl"/> </Dataset> </Query> Similar errors arise if one attempts the same query through the web interface. E.g., for MEROPS: Serious Error: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_MEROPS__dm.translation_id_1068_key' in 'where clause' ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_MEROPS__dm.translation_id_1068_key' in 'where clause' 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 /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Dataset/TableSet.pm:241 BioMart::Dataset::TableSet::_fillAttributeTableWith /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124 BioMart::Dataset::TableSet::_getResultTable /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/DatasetI.pm:1170 BioMart::DatasetI::getResultTable /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/QueryRunner.pm:472 BioMart::QueryRunner::_processPath /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/QueryRunner.pm:374 BioMart::QueryRunner::_getResultTable /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/QueryRunner.pm:194 BioMart::QueryRunner::execute /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Web.pm:2461 (eval) /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Web.pm:2213 BioMart::Web::handle_request /ensemblweb/wwwmart/www_59/biomart-perl/cgi-bin/martview:100 (eval) /ensemblweb/wwwmart/www_59/biomart-perl/cgi-bin/martview:99 ModPerl::ROOT::ModPerl::Registry::ensemblweb_wwwmart_www_59_biomart_2dperl_cgi_2dbin_martview::handler /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204 (eval) /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204 ModPerl::RegistryCooker::run /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170 ModPerl::RegistryCooker::default_handler /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:31 ModPerl::Registry::handler -e:0 (eval) -e:0 Thanks! Gabriel ============================================================= Gabriel F. Berriz, PhD Senior Bioinformatics Developer Roth Lab Biological Chemistry and Molecular Pharmacology -- Harvard Medical School 250 Longwood Avenue Seeley G. Mudd Building 322B Boston, MA 02115-5701 Telephone: 617.432.3555 Fax: 617.432.3557
