Hi Francesco,
Please see an email from Rhoda explaining the issue on mart-dev:

http://listserver.ebi.ac.uk/mailing-lists-archives/mart-dev/msg02335.html

A.


On 23/07/09 5:19 AM, "FRANCESCO GANDOLFI" <[email protected]>
wrote:

> Dear Dr.Arek Kasprzyk,
> 
> I'm reporting a likely bug of the BioMart web site.
> 
> I have tried to use MartView to download the list of ENSEMBL TRANSCRIPT
> and EXON IDs related to the full list of ENSEMBL GENE IDs for the Rattus
> Norvegicus genome. The web interface returns an error message during the
> results retrieval.
> 
> The same error occured when I tried the same query on a selected sublist
> of ENSEMBL GENE IDs.
> 
> The error does not seem to me very clear, but I suppose it is due to a
> missing database file.
> 
> 
> I'm reporting below the exact parameters used in my query along with the
> full error messsage.
> 
> Please let me know if you can fix this bug.
> Thank you in advance.
> 
> Francesco Gandolfi
> 
> 
> 
> 
> ### PARAMETERS USED FOR THE QUERY ON MARTVIEW
> 
> DATASET
> -Ensembl 55 Genes (as database)
> -Rattus Norvegicus Genes (as dataset)
> 
> ATTRIBUTES - structure
> Ensembl Gene ID
> Ensembl Transcript ID
> Ensembl Exon ID
> 
> 
> 
> ### ERROR MESSAGE
> 
> Serious Error: Error during query execution: Can't find file:
> './ensembl_mart_55/rnorvegicus_gene_ensembl__exon_transcript__dm.frm'
> (errno: 13)
> 
> ERROR: caught BioMart::Exception::Database: Error during query execution:
> Can't find file:
> './ensembl_mart_55/rnorvegicus_gene_ensembl__exon_transcript__dm.frm'
> (errno: 13)
> 
> 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:2
> 41
> BioMart::Dataset::TableSet::_fillAttributeTableWith
> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/TableSet.pm:1
> 24
> BioMart::Dataset::TableSet::_getResultTable
> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/DatasetI.pm:1170
> BioMart::DatasetI::getResultTable
> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:472
> BioMart::QueryRunner::_processPath
> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:374
> BioMart::QueryRunner::_getResultTable
> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:194
> BioMart::QueryRunner::execute
> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2433
> (eval) /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2201
> BioMart::Web::handle_request
> /srv/biomart_server/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_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
> 
> 

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