Hi Michal, I am switching to english because we will need help from Ensembl people and/or Steffen Durinck who is the biomaRt author and maintainer. (i am cc'ing your email the the [email protected] mailing list).
Rhoda and Steffen: There seems to be an error caused by a missing table. It looks like biomaRt is out of sync with it's config? or is it Ensembl mart that is out of sync with its tables? a 2011/10/12 Michal Okoniewski <[email protected]> > Hej Arek, > > Pracuje duzo uzywajac Ensembla i Biomarta, zazwyczaj dziala super. Dzis > musialem zejsc na psy, czyli na Canis Familiaris, żeby zamienic RefSeq dla > psa na ortologi EnsemblID czlowieka. > > biomaRt w R mowi: > > getBM(attributes = c("human_ensembl_gene"), filters = "refseq_mrna", > + values = "NM_001017519", mart = ensembl)[[1]] > Error in getBM(attributes = c("human_ensembl_gene"), filters = > "refseq_mrna", : > Query ERROR: caught BioMart::Exception::Database: Error during query > execution: Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist > > choc getFilters podaja, ze jest "refseq_mrna" a konwersja ENSpies => > ENSczlowiek przebiega swietnie a lista ortologow jest duuuzo pelniejsza niż > kilka lat temu :) > > webowy interface mowi w zasadzie to samo: > > 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<http://biomart.org/biomart-perl/cgi-bin/martview:95%0AModPerl::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 > > > Baza psa nie ma RefSeq'a czy to jakis chwilowy blad? > > > Dziekuje, pozdrawiam, > > Michal > > > Michal > -- > -- > > Dr. Michal Okoniewski > Functional Genomics Center Zurich > Winterthurerstrasse 190 > 8057 Zurich, Switzerland > > Phone: +41 44 635 39 24 > Fax: +41 44 635 39 22 > >
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