[BioMart Users] error when trying to extract info using nm_ IDs

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[BioMart Users] error when trying to extract info using nm_ IDs

Dalgliesh, Gillian

Hi there,

 

I have been trying to extract data using a list of NM_ IDs and get the following error even if only typing in the single example identifier (NM_001195597).

 

Is this something you could help with?

 

 

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

 

Thanks,

 

Gillian

 

Gillian L. Dalgliesh

_____________________________________________________________________________________________

 

AstraZeneca

PHB | Genetics

19G22, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK.

T: +44 (0)1625 518781  Internal: 28781

[hidden email]  

 


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Re: [BioMart Users] error when trying to extract info using nm_ IDs

Rhoda Kinsella
Hi Gillian,
This is a known bug in the configuration of these filters and will be rectified for release 65 due out in November. 

See here for more information:

I have fixed the bug on an internal test website and am happy to run your query for you and forward the results. Apologies for an inconvenience.
Regards
Rhoda


On 12 Oct 2011, at 15:29, Dalgliesh, Gillian wrote:


Hi there,
 
I have been trying to extract data using a list of NM_ IDs and get the following error even if only typing in the single example identifier (NM_001195597).
 
Is this something you could help with?
 
 
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

 

Thanks,
 
Gillian
 
Gillian L. Dalgliesh
_____________________________________________________________________________________________
 
AstraZeneca
PHB | Genetics
19G22, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK.
T: +44 (0)1625 518781  Internal: 28781
 




AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD.


Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful.


Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email.


Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking compliance with our Code of Conduct and policies.














_______________________________________________
Users mailing list
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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.


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