getBM query to useEnsembl(biomart="snp"..) not responding
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phpaul2010 • 0
@phpaul2010-11177
Last seen 6.5 years ago

The R script below worked several days ago, for the past two days  it hangs or occasionally returns 

Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

R libraries and biconductor libraries  updated with no effect. 

Suggestions? 

library(biomaRt)

variation = useEnsembl(biomart="snp", dataset="hsapiens_snp")

px <- c("rs11432677","rs632952","rs60178352","rs174686","rs201456215")

ppx <- getBM(attributes=c('refsnp_id','chr_name','chrom_start','chrom_end',"ensembl_peptide_allele",
                          'ensembl_gene_stable_id','ensembl_transcript_stable_id'), 
             filters = 'snp_filter', values =px, mart = variation)

 

bioconductor • 913 views
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I can confirm I'm experiencing the same issues.  I see the same problem if I use one the Ensembl mirror sites, or the web interface to carry out the query, which suggests to me that it's an issue with the databae, rather than the web interface.  If that's the case then there isn't really anything we can 'fix' in biomaRt, but I'll keep look at the issue.

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Mike Smith ★ 6.5k
@mike-smith
Last seen 26 minutes ago
EMBL Heidelberg

This should now be fixed (https://groups.google.com/forum/?fromgroups#!topic/biomart-users/ckiglj9Og6A)

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