Hi Francesco, Please see an email from Rhoda explaining the issue on mart-dev:
http://listserver.ebi.ac.uk/mailing-lists-archives/mart-dev/msg02335.html A. On 23/07/09 5:19 AM, "FRANCESCO GANDOLFI" <[email protected]> wrote: > Dear Dr.Arek Kasprzyk, > > I'm reporting a likely bug of the BioMart web site. > > I have tried to use MartView to download the list of ENSEMBL TRANSCRIPT > and EXON IDs related to the full list of ENSEMBL GENE IDs for the Rattus > Norvegicus genome. The web interface returns an error message during the > results retrieval. > > The same error occured when I tried the same query on a selected sublist > of ENSEMBL GENE IDs. > > The error does not seem to me very clear, but I suppose it is due to a > missing database file. > > > I'm reporting below the exact parameters used in my query along with the > full error messsage. > > Please let me know if you can fix this bug. > Thank you in advance. > > Francesco Gandolfi > > > > > ### PARAMETERS USED FOR THE QUERY ON MARTVIEW > > DATASET > -Ensembl 55 Genes (as database) > -Rattus Norvegicus Genes (as dataset) > > ATTRIBUTES - structure > Ensembl Gene ID > Ensembl Transcript ID > Ensembl Exon ID > > > > ### ERROR MESSAGE > > Serious Error: Error during query execution: Can't find file: > './ensembl_mart_55/rnorvegicus_gene_ensembl__exon_transcript__dm.frm' > (errno: 13) > > ERROR: caught BioMart::Exception::Database: Error during query execution: > Can't find file: > './ensembl_mart_55/rnorvegicus_gene_ensembl__exon_transcript__dm.frm' > (errno: 13) > > 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:2 > 41 > BioMart::Dataset::TableSet::_fillAttributeTableWith > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/TableSet.pm:1 > 24 > 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_2dp > erl_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 > >
