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Question: Error in getBM of biomaRt package
1
gravatar for rubi
2.1 years ago by
rubi90
rubi90 wrote:

Hi,

This type of error was already posted BioMart connection problem but I don't see that it was resolved.

 

I've been using this code for a while:

require(biomaRt,quietly=T)

mart <- useMart(biomart="ensembl",dataset = "hsapiens_gene_ensembl")

df <- getBM(attributes = c("ensembl_gene_id"),mart=mart)

with no problems but now all of a sudden I'm getting this error:

Error in getBM(attributes = c("ensembl_gene_id"), mart = mart) : 

 

  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_87: DBI connect('database=ensembl_mart_87;host=ensdbweb-1-vip;port=5316','ensro',...) failed: Too many connections at /ensemblweb/wwwmart/www_87/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.

 

This persists even if change my code to:

mart <- useMart(biomart="ensembl",dataset = as.character(data.set),host="www.ensembl.org")

or:

mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",dataset = as.character(data.set),host="www.ensembl.org")

 

Any idea?

 

biomart getbm • 1.1k views
ADD COMMENTlink modified 23 months ago by boris.steipe0 • written 2.1 years ago by rubi90

I am having this exact same issue today, and I've been unable to resolve it. Is this still thought to be related to DOS attacks?

ADD REPLYlink modified 23 months ago • written 23 months ago by longoka0
Answer: Error in getBM of biomaRt package
2
gravatar for Mike Smith
2.1 years ago by
Mike Smith3.3k
EMBL Heidelberg / de.NBI
Mike Smith3.3k wrote:

I'm pretty certain this error is related to issues with the Ensembl biomart server, but I'm currently not seeing this when I run your code, so maybe it's been fixed already. 

If you experience it again, you can always try one of the Ensembl mirror sites to see if they're working, like this:

mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", 
                dataset = "hsapiens_gene_ensembl", 
                host = "useast.ensembl.org")

You can also use asia.ensembl.org and uswest.ensembl.org for the host argument.

ADD COMMENTlink written 2.1 years ago by Mike Smith3.3k
Answer: Error in getBM of biomaRt package
1
gravatar for abhi.amarnani
23 months ago by
abhi.amarnani10 wrote:

Unfortunately, it looks like the main ensembl.org server doesn't work either - at least for me. Throughout this weekend I have been having the same error with what looks like the communication error with BioMart to annotate my data.  Does anyone have a solution for this? or if not, a way to revert to the earlier version somehow so BioMart can be used?

 

source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
require(biomaRt)

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                         dataset = "mmusculus_gene_ensembl",
                         host = 'ensembl.org')

t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id",
                                     "external_gene_name","chromosome_name", "entrezgene",
                                     "ucsc"), mart = mart)

Output then is:

Error in biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id",  : 
  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_87: DBI connect('database=ensembl_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.

 

ADD COMMENTlink written 23 months ago by abhi.amarnani10

If you're asking a new question, it's a better idea to create a new post on this site rather than to create a 'answer' to an existing question, or to write a comment if you're adding extra information to someone else's post.

You code works fine for me (at "2017-04-03 09:54:00 CEST"), so maybe the issue has been fixed on the Ensembl side.  If you're still having problems, you can try using an archive.  The most recent is Ensembl 87, which you can use by specifying the appropriate host to useMart() e.g.

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                         dataset = "mmusculus_gene_ensembl",
                         host = 'dec2016.archive.ensembl.org')

 

ADD REPLYlink modified 23 months ago • written 23 months ago by Mike Smith3.3k

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

ADD REPLYlink written 23 months ago by Thomas Maurel770
Answer: Error in getBM of biomaRt package
0
gravatar for Thomas Maurel
2.0 years ago by
Thomas Maurel770
United Kingdom
Thomas Maurel770 wrote:

Hello,

I am afraid that we had a DOS attack affecting our www.ensembl.org marts on Friday.

The services were restored shortly after the attack.

Apologies for any inconveniences caused. 

Kind Regards,

Thomas

ADD COMMENTlink written 2.0 years ago by Thomas Maurel770

I am having this exact same issue today (3-31-2017) using the 'getBM' fucntion, and I've been unable to resolve it. Is this still thought to be related to DOS attacks?

ADD REPLYlink modified 23 months ago • written 23 months ago by longoka0

I noticed same issue when trying to access information via the useast.esemble.org biomart browser; output below:

Serious Error: Could not connect to mysql database ensembl_mart_87: DBI connect('database=ensembl_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.

ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_87: DBI connect('database=ensembl_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.

ADD REPLYlink modified 23 months ago • written 23 months ago by longoka0

Ensembl was updated to version 88 a couple of days ago (Ensembl 88 is out!), and the mirrors lag a little behind.  Perhaps you've been caught in the transition.  You can certainly see references to both 87 and 88 in your error messages.

My suggestion would be to use the main www.ensembl.org server for the moment, and try the mirror again in a day or so.

ADD REPLYlink modified 23 months ago • written 23 months ago by Mike Smith3.3k

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

ADD REPLYlink written 23 months ago by Thomas Maurel770

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

ADD REPLYlink written 23 months ago by Thomas Maurel770
Answer: Error in getBM of biomaRt package
0
gravatar for boris.steipe
23 months ago by
Canada
boris.steipe0 wrote:

I saw the same error yesterday - it went away this morning. There was no note of an outage on the blog, but it looks like that's what it was.

ADD COMMENTlink written 23 months ago by boris.steipe0
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