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ERROR: caught BioMart::Exception: non-BioMart die(): Can't locate object method "setTable" via package "BioMart::Configuration::Attribute" at /nfs/public/ro/ensweb/live/mart/www_111/biomart-perl/lib/BioMart/Query.pm line 1321.
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Stacktrace:
Exception::Class::Base::new /nfs/public/ro/ensweb/live/mart/www_111/ensembl-webcode/biomart-perl/cgi-bin/martview:107
ModPerl::ROOT::ModPerl::Registry::nfs_public_ro_ensweb_live_mart_www_111_ensembl_2dwebcode_biomart_2dperl_cgi_2dbin_martview::handler /nfs/public/ro/ensweb-software/sharedsw/2022_01_17_ct7/linuxbrew/Cellar/perl/5.34.0/lib/perl5/site_perl/5.34.0/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:207
(eval) /nfs/public/ro/ensweb-software/sharedsw/2022_01_17_ct7/linuxbrew/Cellar/perl/5.34.0/lib/perl5/site_perl/5.34.0/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:207
ModPerl::RegistryCooker::run /nfs/public/ro/ensweb-software/sharedsw/2022_01_17_ct7/linuxbrew/Cellar/perl/5.34.0/lib/perl5/site_perl/5.34.0/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:173
ModPerl::RegistryCooker::default_handler /nfs/public/ro/ensweb-software/sharedsw/2022_01_17_ct7/linuxbrew/Cellar/perl/5.34.0/lib/perl5/site_perl/5.34.0/x86_64-linux-thread-multi/ModPerl/Registry.pm:32
ModPerl::Registry::handler -e:0
(eval) -e:0
When trying to get the sequence and one base upstream using biomaRt ...
seq = getSequence(id = "ENSG00000006062",
type = "ensembl_gene_id",
seqType = "gene_exon_intron",
upstream=1,
mart = ensembl)[["gene_exon_intron"]]
... I get the following error:
Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, :
Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND
This error is misleading. I would have expected biomaRt to catch the actual error and print it. Please also consider (especially thinking about larger collection of genes or gene retrieval in a loop) a parameter IGNORE that would make R continue execution upon encountering this error.
The text was updated successfully, but these errors were encountered:
The Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND is actually directly obtained from the BioMart server, so I'm not sure it can be classed as misleading. Here's an example omitting biomaRt and just using wget to submit the relevant XML query:
-> % wget -q -O result.txt 'https://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query virtualSchemaName = "default" uniqueRows="1" count="0" datasetConfigVersion="0.6" header="1" formatter="TSV" requestid="biomaRt"> <Dataset name="hsapiens_gene_ensembl"> <Attribute name = "gene_exon_intron"/> <Attribute name = "ensembl_gene_id"/> <Filter name = "ensembl_gene_id" value = "ENSG00000006062" /> <Filter name = "upstream_flank" value = "1" /> </Dataset></Query>'
-> % cat result.txt
Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND
Interestingly you now seem to get a different error if you don't include the upstream flank filter:
-> % wget -q -O result.txt 'https://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query virtualSchemaName = "default" uniqueRows="1" count="0" datasetConfigVersion="0.6" header="1" formatter="TSV" requestid="biomaRt"> <Dataset name="hsapiens_gene_ensembl"> <Attribute name = "gene_exon_intron"/> <Attribute name = "ensembl_gene_id"/> <Filter name = "ensembl_gene_id" value = "ENSG00000006062" /> </Dataset></Query>'
-> % cat result.txt
Query ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable?
This matches what get's printed to screen when trying to use the web UI. Ultimately it looks like this functionality is broken in the Ensembl BioMart server.
Hello,
the gene in question is ENSG00000006062.
I can retrieve its full sequence fine, but I cannot retrieve upstream of it (for whatever reason).
The error I get from the website is (https://www.ensembl.org/biomart/martview/73d235843385abf343bae7c7ae330404):
When trying to get the sequence and one base upstream using biomaRt ...
... I get the following error:
This error is misleading. I would have expected biomaRt to catch the actual error and print it. Please also consider (especially thinking about larger collection of genes or gene retrieval in a loop) a parameter
IGNORE
that would make R continue execution upon encountering this error.The text was updated successfully, but these errors were encountered: