Query Error: biomaRt
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@jaspreet-kaur-12425
Last seen 7.0 years ago

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.

biomart bioconductor • 1.5k views
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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

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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

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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

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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 away

 

thanks

Jennifer

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