[ensembl-dev] Error during query execution using Refseq mRNA IDs as Filter

[Rhoda Kinsella]

Hi Johannes
This is a known bug (please see here: http://www.ensembl.info/contact-us/known-bugs/) 
. This known bugs page includes a temporary workaround. Unfortunately  
we will not be able to make the bug fix live until our next release 65  
due out in November. I have, however, fixed this on an internal server  
and am happy to run your query for you if you send me your list of  
query RefSeq IDs.
I hope that helps,
Regards
Rhoda




On 6 Oct 2011, at 15:16, Johannes Meisig wrote:

> Hi,
>
> a month I started using Ensembl/Biomart to find Ensembl Gene IDs
> corresponding to Refseq IDs. When I tried it again yesterday it didn't
> work anymore.
>
> Selecting Ensembl Gene ID and Ensembl Transcript ID as attributes and
> Refseq mRNA ID with the Mus musculus genes dataset I get the error
> attached to this message on the website.
>
> The error can be easily reproduced by plugging in the example ID
> NM_01195597 into the ID list. Is this problem known? Is there  
> anything I
> should do differently?
>
> Thanks,
> Johannes
>
> 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
> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Dataset/ 
> TableSet.pm:241
> BioMart::Dataset::TableSet::_fillAttributeTableWith
> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Dataset/ 
> TableSet.pm:124
> BioMart::Dataset::TableSet::_getResultTable
> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/DatasetI.pm:1170
> BioMart::DatasetI::getResultTable
> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/QueryRunner.pm:472
> BioMart::QueryRunner::_processPath
> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/QueryRunner.pm:374
> BioMart::QueryRunner::_getResultTable
> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/QueryRunner.pm:194
> BioMart::QueryRunner::execute
> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Web.pm:2464
> (eval) /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Web.pm:2216
> BioMart::Web::handle_request
> /ensemblweb/wwwmart/www_64/biomart-perl/cgi-bin/martview:100
> (eval) /ensemblweb/wwwmart/www_64/biomart-perl/cgi-bin/martview:99
> ModPerl 
> ::ROOT 
> ::ModPerl 
> ::Registry 
> ::ensemblweb_wwwmart_www_64_biomart_2dperl_cgi_2dbin_martview::handler
> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/ 
> RegistryCooker.pm:204
> (eval)
> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/ 
> RegistryCooker.pm:204
> ModPerl::RegistryCooker::run
> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/ 
> RegistryCooker.pm:170
> ModPerl::RegistryCooker::default_handler
> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/ 
> Registry.pm:31
> ModPerl::Registry::handler -e:0
> (eval) -e:0
>
>
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Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

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