Thanks Arek. Looks like missing table(s) indeed. All the queries dog Refseq => human orthologs that I tried today behave like that.
Cheers, M From: Arek Kasprzyk <[email protected]<mailto:[email protected]>> Date: Wed, 12 Oct 2011 08:57:09 -0400 To: Michal Okoniewski <[email protected]<mailto:[email protected]>> Cc: <[email protected]<mailto:[email protected]>>, Steffen Durinck <[email protected]<mailto:[email protected]>> Subject: Re: dog biomart + refseq problem 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]<mailto:[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]<mailto:[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<http://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<http://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<http://biomart.org/biomart-perl/lib/BioMart/DatasetI.pm:1170> BioMart::DatasetI::getResultTable /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:472<http://biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:472> BioMart::QueryRunner::_processPath /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:374<http://biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:374> BioMart::QueryRunner::_getResultTable /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:194<http://biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:194> BioMart::QueryRunner::execute /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2433<http://biomart.org/biomart-perl/lib/BioMart/Web.pm:2433> (eval) /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2201<http://biomart.org/biomart-perl/lib/BioMart/Web.pm:2201> BioMart::Web::handle_request /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:96<http://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<tel:%2B41%2044%20635%2039%2024> Fax: +41 44 635 39 22<tel:%2B41%2044%20635%2039%2022> _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
