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:
http://www.ensembl.info/contact-us/known-bugs/
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 [email protected]
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 <[email protected]>
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: +41 44 635 39 24
Fax: +41 44 635 39 22
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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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