Error in getBM of biomaRt package
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rubi ▴ 100
@rubi-6462
Last seen 3.2 years ago

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 • 3.3k views
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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?

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Mike Smith ★ 5.2k
@mike-smith
Last seen 6 hours ago
EMBL Heidelberg / de.NBI

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.

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@abhiamarnani-12744
Last seen 4.6 years ago

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.

 

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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')

 

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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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Thomas Maurel ▴ 790
@thomas-maurel-5295
Last seen 12 weeks ago
United Kingdom

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

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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?

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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.

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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.

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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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Entering edit mode

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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@borissteipe-7050
Last seen 4.6 years ago
Canada

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.

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