Hi Daniel, apologies for the late reply.
Could you please check if it works for you today ? thanks Syed On 26/05/2010 13:27, Daniel Barrell wrote:
Hi, I'm trying to use biomart to get protein coding sequences in fasta format with ensembl gene and peptide identifiers in the ID line for 8 species. I was doing this via the API but consistently got http 500 and 502 errors yesterday. This morning I discovered how you could run a job in the background via the web site and get the compressed results emailed to you in a link. This worked a couple of times and now I am consistently getting the following error: ERROR: caught BioMart::Exception: non-BioMart die(): Can't locate object method "error" via package "Cannot fork: Cannot allocate memory " (perhaps you forgot to load "Cannot fork: Cannot allocate memory "?) at /ensemblweb/wwwmart/www_57/biomart-perl/lib/BioMart/Web.pm line 2516. 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::new /ensemblweb/wwwmart/www_57/biomart-perl/cgi-bin/martview:106 ModPerl::ROOT::ModPerl::Registry::ensemblweb_wwwmart_www_57_biomart_2dperl_cgi_2dbin_martview::handler /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204 (eval) /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204 ModPerl::RegistryCooker::run /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170 ModPerl::RegistryCooker::default_handler /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:31 ModPerl::Registry::handler -e:0 (eval) -e:0 Is this something that can be fixed your end or am I doing something wrong? Cheers Dan PS: here's the setup I was using @ ensembl.org/biomart Dataset Bos taurus genes (Btau_4.0) Bos taurus genes (Btau_4.0) Filters Gene type : protein_coding Attributes Ensembl Gene ID Ensembl Transcript ID [2 enabled] Ensembl Gene ID Ensembl Transcript ID [2 enabled][2 enabled] Ensembl Gene ID Ensembl Transcript ID [2 enabled][2 enabled] Ensembl Gene ID Ensembl Transcript ID Reference ID [3 enabled][3 enabled] Peptide Ensembl Gene ID [3 enabled] Ensembl Protein ID Dataset [None Selected]
