Hi Arek and Hendrik
Yes this is a known bug (see http://www.ensembl.info/contact-us/known-bugs/)
and we will fix this for release 65 due out in November. If you
would like us to run your query for you, then please send us your list
of ID's and we will run this query on our internal server. Apologies
for any inconvenience caused.
Regards
Rhoda
On 3 Nov 2011, at 16:22, Arek Kasprzyk wrote:
Hi Hendrik,
i believe this issue has been reported on the list before and (Rhoda
to correct me here)that it is going to be
fixed in the next Ensembl release?
a
Dear Biomart team,
I have entered the following request into the Biomart interface
http://www.biomart.org/biomart/martview/
Dataset: Homo sapiens genes (GRCh37.p5)
Filters: Refseq mRNA ID(s) [e.g. NM_001195597]: [ID-list specified]
-->
with NM_000211 in the list
Attributes: Ensembl Gene ID, Ensembl Transcript ID
But I get always the following error message:
----------------
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
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/
TableSet.pm:241
BioMart::Dataset::TableSet::_fillAttributeTableWith
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/
TableSet.pm:124
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_2dperl_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
------------------
How do I get a Refseq/Ensembl id mapping?
Thanks for any help.
Regards,
Hendrik
--
Always Outnumbered, Never Outgunned
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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