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

[Johannes Meisig]

Hi Rhoda,

thanks for answering so quickly! As a workaround, I make the database 
query the other way around. It's a bit slower because I have to plug in 
the whole genome now, but that's not a big problem.

Johannes

Rhoda Kinsella wrote:
> 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.
>