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]
