Hi Matthew, Could you send us an XML version of this query to help us debug it please?
Please set up your query as normal using MartView interface and then press XML button in the top right hand corner. Please copy and paste what's there into an email and send it to us Cheers, A. On 21/07/09 8:29 PM, "Matthew Strand" <[email protected]> wrote: > 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=ENSDARG > 00000059654;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.pm > <http://biomart.org/biomart-perl/lib/BioMart/Query.pm> line 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 > <http://biomart.org/biomart-perl/lib/BioMart/Query.pm> line 1716. > "?) at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm > <http://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 > <http://biomart.org/biomart-perl/cgi-bin/martview:101> > 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 > > --- > Matthew Strand
