Hi,
I have been trying to retrieve variant information using biomaRt function getBM but I am getting a query error which states biomaRt database cannot be connected to mysql database "snp_mart_87". It will be great if I can get answer to this particular query. I am using following code:
> library(biomaRt)
> mart_snp<- useMart("ENSEMBL_MART_SNP", dataset = "hsapiens_snp", host = "www.ensembl.org")
> val<- c("rs1799971", "rs1799972", "rs9282818")
> result<- biomaRt::getBM(attributes = c("chr_name","minor_allele_freq", "refsnp_id" , "pmid") , values = val, mart = mart_snp)
ERROR OBTAINED
Error in biomaRt::getBM(attributes = c("chr_name", "minor_allele_freq", :
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database snp_mart_87: DBI connect('database=snp_mart_87;host=ensdbweb-1-vip;port=5316','ensro',...) failed: Unknown MySQL server host 'ensdbweb-1-vip' (1) at /ensemblweb/www/www_88/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
This looks like you're getting the same error reported in C: Error in getBM of biomaRt package
Ensembl was updated to version 88 a couple of days ago (Ensembl 88 is out!), and I suspect this is related to that. You can certainly see references to both 87 and 88 in your error messages. Running your code currently just hangs my R session when I try it (I gave up after 30 minutes wait).
Interestingly it seems to work fine if you use the web interface for your query here
Hello,
Thank you for letting us know. We are looking into fixing this issue as soon as possible. I will let you know once the issue is resolved.
Apologies for any inconvenience caused.
Kind Regards,
Thomas
Hello,
The issue has now been fixed. Please let me know if you are still having problems.
Apologies for any inconvenience caused.
Kind Regards,
Thomas
Hi I have been having a similar problem and I still can't conect.
Error in getBM(attributes = c("ensembl_gene_id", "entrezgene", "external_gene_name"), : Query ERROR: caught BioMart::Exception::Database: Error during query execution: MySQL server has gone awaythanks
Jennifer