[BioC] too many biomaRt connections

[Steffen]

Hi Elizabeth,

This is an error I've recently encountered as well and has as far as I 
know nothing to do with the number of queries you performed but is a 
more general problem of the BioMart version of Ensembl.
biomaRt is not the only tool querying this web service.  Other tools 
like Taverna and custom tools using e.g. the BioMart perl API also query 
this web service. 
It looks like the BioMart system has gained popularity and recently we 
frequently hit the maximum number of connections to the MySQL database.  
Note that biomaRt doesn't query directly via MySQL but it's the MySQL 
connection at the web service that is unable to connect.

I've contacted the Ensembl and BioMart teams and they are investigating 
this problem.  It would help reporting this to helpdesk at ensembl.org to 
pressure them on this issue, showing it's not only me but many people 
who can't use their web service recently.  Report this part of the error 
message:

Too many connections at 
/ebi/www/biomart/www/biomart-perl-06/lib/BioMart/Configuration/DBLocation.pm 
line 98


Cheers,
Steffen

Elizabeth Purdom wrote:
> Hi,
> I am using biomaRt to get information regarding genes. I use it pretty 
> frequently and recently have gotten the error:
>
> Too many connections at 
> /ebi/www/biomart/www/biomart-perl-06/lib/BioMart/Configuration/DBLocation.pm 
> line 98
>
> I assume that I've hit some sort of wall in terms of how often I have 
> queried the database?
>
> I don't really use biomart except through R; at what point do you get 
> booted off and what can I do to regain access? I often run queries on a 
> few hundred genes and don't think twice about rerunning such a query or 
> running several such queries in a day plus I use functions that call on 
> biomaRt repeatedly that I also apply to around 100 genes. So I could 
> easily send a thousand queries in a day. I can be more careful, but it 
> would be useful to know what the limits are. And does it matter how many 
> times you call a 'mart<-useMart(...)' command? (lately, I've been 
> calling it frequently rather than using the one I've already opened, 
> largely through programming laziness).
>
> By the way, it took me quite some time to track down the error, because 
> I was using getGene which just gave me the confusing error:
> "Error: ncol(result) == length(attributes) is not TRUE"
> I think this must be because something like try(...) is used within 
> getBM() and so the output is the error message which is then transferred 
> down the line and at some point causes a problem when the function tries 
> to bundle it into a data.frame, etc.
>
> Thanks,
> Elizabeth
>
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-- 
----------------------------------------------------------------
Steffen Durinck, PhD

Division of Biostatistics, University of California, Berkeley &
Life Sciences Department, Lawrence Berkeley National Laboratory
1 cyclotron Rd, Berkeley
CA, 94720, USA
Tel: +1-510-486-5202