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.
