Hi, I've been using BioMart to retrieve sequences given a speices name and Ensembl protein ID. Recently many queries that worked before began failing.
This can be reproduced in MartView as follows: Database: ENSEMBL 55 GENES (SANGER UK) Dataset: Danio rerio genes Filters: GENE>ID list limit > Ensembl protein ID(s): ENSDARP00000077564 Attributes: Sequences Executing Count shows 1 match is present. The error message is shown below. This error occurs with several of my proteins. This is just an example. Can anyone help me resolve this? Assistance would be much appreciated. The sequence is available on the web with no problem at: http://www.ensembl.org/Danio_rerio/Transcript/ProteinSummary?db=core;g=ENSDARG00000059654;r=3:38838155-38847525;t=ENSDART00000083129 Executing results returns: ERROR: caught BioMart::Exception: non-BioMart die(): Can't locate object method "error" via package "Can't call method "defaultLink" on an undefined value at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Query.pmline 1716. " (perhaps you forgot to load "Can't call method "defaultLink" on an undefined value at /srv/biomart_server/ biomart.org/biomart-perl/lib/BioMart/Query.pm line 1716. "?) at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm line 2488. 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::new /srv/biomart_server/ biomart.org/biomart-perl/cgi-bin/martview:101 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 --- Matthew Strand
