Hi Rhoda and Martin,
the bug clearly suggests that the following table is either corrupt or
does not exist:
snp_mart_52.hsapiens_snp__transcript_variation__dm
the ensembl databases (snp_mart_52 in this case) are hosted at
(martdb.ensembl.org:5316) and are run and managed by Ensembl team (web
team), so they need to fix the table.
The reason it works fine for ensembl.org is that the ensembl.org's
BioMart installation runs on another internal ensembl databases server
while Biomart.org runs on public db server(martdb.ensembl.org:5316).
Cheers
Syed
Rhoda Kinsella wrote:
Hi Biomart team,
A BioConductor user has reported a bug in the Ensembl 52 Variation
database on biomart.org. This bug does not appear on the ensembl.org
mart interface.
If you select Ensembl 52 variation database and species Homo sapiens.
Select RefSNP ID-> rs10399749 from the General SNP filters (Limit to
SNPs with these IDs).
Select Ensembl Gene ID from the SNPs->Gene SNP Attributes and hit results.
You get the following error:
Serious Error: Error during query execution: File
'./snp_mart_52/hsapiens_snp__transcript_variation__dm.MYD' not found
(Errcode: 27)
ERROR: caught BioMart::Exception::Database: Error during query
execution: File
'./snp_mart_52/hsapiens_snp__transcript_variation__dm.MYD' not found
(Errcode: 27)
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
/ebi/www/biomart/www/biomart-perl-07/lib/BioMart/Dataset/TableSet.pm:241
BioMart::Dataset::TableSet::_fillAttributeTableWith
/ebi/www/biomart/www/biomart-perl-07/lib/BioMart/Dataset/TableSet.pm:124
BioMart::Dataset::TableSet::_getResultTable
/ebi/www/biomart/www/biomart-perl-07/lib/BioMart/DatasetI.pm:1170
BioMart::DatasetI::getResultTable
/ebi/www/biomart/www/biomart-perl-07/lib/BioMart/QueryRunner.pm:481
BioMart::QueryRunner::_processPath
/ebi/www/biomart/www/biomart-perl-07/lib/BioMart/QueryRunner.pm:383
BioMart::QueryRunner::_getResultTable
/ebi/www/biomart/www/biomart-perl-07/lib/BioMart/QueryRunner.pm:203
BioMart::QueryRunner::execute
/ebi/www/biomart/www/biomart-perl-07/lib/BioMart/Web.pm:2429
(eval) /ebi/www/biomart/www/biomart-perl-07/lib/BioMart/Web.pm:2197
BioMart::Web::handle_request
/ebi/www/biomart/www/biomart-perl-07/cgi-bin/martview:101
(eval) /ebi/www/biomart/www/biomart-perl-07/cgi-bin/martview:100
ModPerl::ROOT::ModPerl::Registry::ebi_www_biomart_www_biomart_2dperl_2d07_cgi_2dbin_martview::handler
/usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:202
(eval)
/usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:202
ModPerl::RegistryCooker::run
/usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:168
ModPerl::RegistryCooker::default_handler
/usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi/ModPerl/Registry.pm:30
ModPerl::Registry::handler -e:0
(eval) -e:0
Kind regards,
Rhoda
Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.
