[BioMart Users] RefSeq mRNAs database error

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[BioMart Users] RefSeq mRNAs database error

Triantafillos Paparountas

I am trying to get a list of unique attributes by uploading a list of RefSeq mRNAs (NM) and wanting to get back

RefSeq mRNAs
Ensembl Gene ID
Ensembl Transcript ID
Ensembl Protein ID
Description
Associated Gene Name
Associated Transcript Name
Gene Biotype
Transcript Biotype
GO Term Accession
GO Term Name
GO Term Definition
Ensembl Family Description
Interpro Description



But this is the answer I am getting: 

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
BioMart::Web::handle_request /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:96
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


--
-----------------------------------------------------------------
    Triantafyllos Paparountas, PhD
    - Bioinformatics Research Assistant
    http://www.bioinformatics.gr
    email: [hidden email]
-----------------------------------------------------------------

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Re: [BioMart Users] RefSeq mRNAs database error

Thomas Maurel
Dear Triantafillos,

This is a known bug in BioMart release 64 : http://www.ensembl.info/contact-us/known-bugs/

This bug will be fixed for release 65 due out in November.
If your query is urgent you can send me your list of your RefSeq mRNAs IDs and I can get the results for you.

Apologies for the inconvenience caused,

Best Regards,
Thomas

On 14 Nov 2011, at 16:11, Triantafillos Paparountas wrote:


I am trying to get a list of unique attributes by uploading a list of RefSeq mRNAs (NM) and wanting to get back

RefSeq mRNAs
Ensembl Gene ID
Ensembl Transcript ID
Ensembl Protein ID
Description
Associated Gene Name
Associated Transcript Name
Gene Biotype
Transcript Biotype
GO Term Accession
GO Term Name
GO Term Definition
Ensembl Family Description
Interpro Description



But this is the answer I am getting: 

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
BioMart::Web::handle_request /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:96
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


--
-----------------------------------------------------------------
    Triantafyllos Paparountas, PhD
    - Bioinformatics Research Assistant
    http://www.bioinformatics.gr
    email: [hidden email]
-----------------------------------------------------------------
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK


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Re: [BioMart Users] RefSeq mRNAs database error

Arek Kasprzyk
In reply to this post by Triantafillos Paparountas
Hi Triantafillos
this is a known problem in the current Ensembl release. Rhoda (cced) on this email will be able to give you an ETA for this fix. BTW, if you skip the RefSeq mRNAs attribute from your output, your query should work fine

a


a

On Mon, Nov 14, 2011 at 11:11 AM, Triantafillos Paparountas <[hidden email]> wrote:

I am trying to get a list of unique attributes by uploading a list of RefSeq mRNAs (NM) and wanting to get back

RefSeq mRNAs
Ensembl Gene ID
Ensembl Transcript ID
Ensembl Protein ID
Description
Associated Gene Name
Associated Transcript Name
Gene Biotype
Transcript Biotype
GO Term Accession
GO Term Name
GO Term Definition
Ensembl Family Description
Interpro Description



But this is the answer I am getting: 

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
BioMart::Web::handle_request /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:96
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


--
-----------------------------------------------------------------
    Triantafyllos Paparountas, PhD
    - Bioinformatics Research Assistant
    http://www.bioinformatics.gr
    email: [hidden email]
-----------------------------------------------------------------

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users