Re: [BioMart Users] dog biomart + refseq problem

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Re: [BioMart Users] dog biomart + refseq problem

Arek Kasprzyk
Hi Michal,
I am switching to english because we will need help from Ensembl people and/or Steffen Durinck who is the biomaRt author and maintainer. (i am cc'ing your email the the [hidden email] mailing list).

Rhoda and Steffen: There seems to be an error caused by a missing table. It looks like biomaRt is out of sync with it's config? or is it Ensembl mart that is out of sync with its tables?


a



2011/10/12 Michal Okoniewski <[hidden email]>
Hej Arek,

Pracuje duzo  uzywajac Ensembla i Biomarta, zazwyczaj dziala super. Dzis musialem zejsc na psy, czyli na Canis Familiaris, żeby zamienic RefSeq dla psa na ortologi EnsemblID czlowieka.

biomaRt w R mowi:

getBM(attributes = c("human_ensembl_gene"), filters = "refseq_mrna",
+ values = "NM_001017519", mart = ensembl)[[1]]
Error in getBM(attributes = c("human_ensembl_gene"), filters = "refseq_mrna",  :
 Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist

choc getFilters podaja, ze jest "refseq_mrna" a konwersja ENSpies => ENSczlowiek przebiega swietnie a lista ortologow jest duuuzo pelniejsza niż kilka lat temu :)

webowy interface mowi w zasadzie to samo:

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


Baza psa nie ma RefSeq'a czy to jakis chwilowy blad?


Dziekuje, pozdrawiam,

Michal


Michal
--
--

Dr. Michal Okoniewski
Functional Genomics Center Zurich
Winterthurerstrasse 190
8057 Zurich, Switzerland

Phone: <a href="tel:%2B41%2044%20635%2039%2024" value="+41446353924">+41 44 635 39 24
Fax: <a href="tel:%2B41%2044%20635%2039%2022" value="+41446353922">+41 44 635 39 22



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Re: [BioMart Users] dog biomart + refseq problem

Michal Okoniewski
Thanks Arek. Looks like missing table(s) indeed. All the queries dog Refseq => human orthologs that I tried today behave like that.

Cheers,
M

From: Arek Kasprzyk <[hidden email]<mailto:[hidden email]>>
Date: Wed, 12 Oct 2011 08:57:09 -0400
To: Michal Okoniewski <[hidden email]<mailto:[hidden email]>>
Cc: <[hidden email]<mailto:[hidden email]>>, Steffen Durinck <[hidden email]<mailto:[hidden email]>>
Subject: Re: dog biomart + refseq problem

Hi Michal,
I am switching to english because we will need help from Ensembl people and/or Steffen Durinck who is the biomaRt author and maintainer. (i am cc'ing your email the the [hidden email]<mailto:[hidden email]> mailing list).

Rhoda and Steffen: There seems to be an error caused by a missing table. It looks like biomaRt is out of sync with it's config? or is it Ensembl mart that is out of sync with its tables?


a



2011/10/12 Michal Okoniewski <[hidden email]<mailto:[hidden email]>>
Hej Arek,

Pracuje duzo  uzywajac Ensembla i Biomarta, zazwyczaj dziala super. Dzis musialem zejsc na psy, czyli na Canis Familiaris, żeby zamienic RefSeq dla psa na ortologi EnsemblID czlowieka.

biomaRt w R mowi:

getBM(attributes = c("human_ensembl_gene"), filters = "refseq_mrna",
+ values = "NM_001017519", mart = ensembl)[[1]]
Error in getBM(attributes = c("human_ensembl_gene"), filters = "refseq_mrna",  :
 Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist

choc getFilters podaja, ze jest "refseq_mrna" a konwersja ENSpies => ENSczlowiek przebiega swietnie a lista ortologow jest duuuzo pelniejsza niż kilka lat temu :)

webowy interface mowi w zasadzie to samo:

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<http://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<http://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<http://biomart.org/biomart-perl/lib/BioMart/DatasetI.pm:1170>
BioMart::DatasetI::getResultTable /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:472<http://biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:472>
BioMart::QueryRunner::_processPath /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:374<http://biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:374>
BioMart::QueryRunner::_getResultTable /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:194<http://biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:194>
BioMart::QueryRunner::execute /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2433<http://biomart.org/biomart-perl/lib/BioMart/Web.pm:2433>
(eval) /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2201<http://biomart.org/biomart-perl/lib/BioMart/Web.pm:2201>
BioMart::Web::handle_request /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:96<http://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<http://biomart.org/biomart-perl/cgi-bin/martview:95%0AModPerl::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


Baza psa nie ma RefSeq'a czy to jakis chwilowy blad?


Dziekuje, pozdrawiam,

Michal


Michal
--
--

Dr. Michal Okoniewski
Functional Genomics Center Zurich
Winterthurerstrasse 190
8057 Zurich, Switzerland

Phone: +41 44 635 39 24<tel:%2B41%2044%20635%2039%2024>
Fax: +41 44 635 39 22<tel:%2B41%2044%20635%2039%2022>


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Re: [BioMart Users] dog biomart + refseq problem

Rhoda Kinsella
In reply to this post by Arek Kasprzyk
Hi Arek and Michal,
This is a known bug with 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 13:57, Arek Kasprzyk wrote:

Hi Michal,
I am switching to english because we will need help from Ensembl people and/or Steffen Durinck who is the biomaRt author and maintainer. (i am cc'ing your email the the [hidden email] mailing list).

Rhoda and Steffen: There seems to be an error caused by a missing table. It looks like biomaRt is out of sync with it's config? or is it Ensembl mart that is out of sync with its tables?


a



2011/10/12 Michal Okoniewski <[hidden email]>
Hej Arek,

Pracuje duzo  uzywajac Ensembla i Biomarta, zazwyczaj dziala super. Dzis musialem zejsc na psy, czyli na Canis Familiaris, żeby zamienic RefSeq dla psa na ortologi EnsemblID czlowieka.

biomaRt w R mowi:

getBM(attributes = c("human_ensembl_gene"), filters = "refseq_mrna",
+ values = "NM_001017519", mart = ensembl)[[1]]
Error in getBM(attributes = c("human_ensembl_gene"), filters = "refseq_mrna",  :
 Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist

choc getFilters podaja, ze jest "refseq_mrna" a konwersja ENSpies => ENSczlowiek przebiega swietnie a lista ortologow jest duuuzo pelniejsza niż kilka lat temu :)

webowy interface mowi w zasadzie to samo:

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


Baza psa nie ma RefSeq'a czy to jakis chwilowy blad?


Dziekuje, pozdrawiam,

Michal


Michal
--
--

Dr. Michal Okoniewski
Functional Genomics Center Zurich
Winterthurerstrasse 190
8057 Zurich, Switzerland

Phone: <a href="tel:%2B41%2044%20635%2039%2024" value="+41446353924">+41 44 635 39 24
Fax: <a href="tel:%2B41%2044%20635%2039%2022" value="+41446353922">+41 44 635 39 22


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

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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Users mailing list
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