[biomart-users] Error in getBM

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[biomart-users] Error in getBM

Stephen Hwang-2
I had a biomaRt query that worked earlier during the week but I get an error now. Is there a problem with my connection?
mart<- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
results <- getBM(filters="illumina_humanht_12_v3", attributes=c("illumina_humanht_12_v3","hgnc_symbol","wikigene_name","description","wikigene_description"), values=combined_probes, mart=mart)


Error in getBM(filters = "illumina_humanht_12_v3", attributes = c("illumina_humanht_12_v3",  : 
  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_85: DBI connect('database=ensembl_mart_85;host=martdb.local.cloud.local;port=3306','ensro',...) failed: Can't connect to MySQL server on 'martdb.local.cloud.local' (111) at /ensemblweb/www/www_85/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.

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[biomart-users] Re: Error in getBM

nadiaatallah1985
I am having the same issue with code that originally worked.  I even changed the host and it still fails to connect

On Thursday, September 22, 2016 at 9:24:20 AM UTC-4, Stephen Hwang wrote:
I had a biomaRt query that worked earlier during the week but I get an error now. Is there a problem with my connection?
mart<- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
results <- getBM(filters="illumina_humanht_12_v3", attributes=c("illumina_humanht_12_v3","hgnc_symbol","wikigene_name","description","wikigene_description"), values=combined_probes, mart=mart)


Error in getBM(filters = "illumina_humanht_12_v3", attributes = c("illumina_humanht_12_v3",  : 
  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_85: DBI connect('database=ensembl_mart_85;host=martdb.local.cloud.local;port=3306','ensro',...) failed: Can't connect to MySQL server on 'martdb.local.cloud.local' (111) at /ensemblweb/www/www_85/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.

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[biomart-users] Re: Error in getBM

francisca.rojas.r
In reply to this post by Stephen Hwang-2
I am getting the same error since yesterday, also on a query that was working fine before:

library(biomaRt)
mart<- useDataset("mmusculus_gene_ensembl", useMart("ensembl"))
gene_names <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id", "external_gene_name"), values=geneIDs, mart=mart)

Error in getBM(filters = "ensembl_gene_id", attributes = c("ensembl_gene_id",  : 
  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_85: DBI connect('database=ensembl_mart_85;host=martdb.local.cloud.local;port=3306','ensro',...) failed: Can't connect to MySQL server on 'martdb.local.cloud.local' (111) at /ensemblweb/www/www_85/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.

I also tried using a different host but I got the same error.

Is there a way around this error?

Thank you very much!

Francisca.

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] VennDiagram_1.6.17  futile.logger_1.4.3 biomaRt_2.28.0     

loaded via a namespace (and not attached):
 [1] IRanges_2.6.1        XML_3.98-1.4         bitops_1.0-6         futile.options_1.0.0
 [5] DBI_0.5-1            stats4_3.3.1         RSQLite_1.0.0        S4Vectors_0.10.3    
 [9] lambda.r_1.1.9       tools_3.3.1          Biobase_2.32.0       RCurl_1.95-4.8      
[13] yaml_2.1.13          parallel_3.3.1       BiocGenerics_0.18.0  AnnotationDbi_1.34.4


On Thursday, September 22, 2016 at 9:24:20 AM UTC-4, Stephen Hwang wrote:
I had a biomaRt query that worked earlier during the week but I get an error now. Is there a problem with my connection?
mart<- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
results <- getBM(filters="illumina_humanht_12_v3", attributes=c("illumina_humanht_12_v3","hgnc_symbol","wikigene_name","description","wikigene_description"), values=combined_probes, mart=mart)


Error in getBM(filters = "illumina_humanht_12_v3", attributes = c("illumina_humanht_12_v3",  : 
  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_85: DBI connect('database=ensembl_mart_85;host=martdb.local.cloud.local;port=3306','ensro',...) failed: Can't connect to MySQL server on 'martdb.local.cloud.local' (111) at /ensemblweb/www/www_85/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.

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[biomart-users] Re: Error in getBM

Dan Staines
We may have had a problem with one of our mirrors though everything seems to be working this morning. Do you know which mirror you were using? (or where you are located in the world)

Thanks,

Dan.


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Re: [biomart-users] Re: Error in getBM

Dan Staines
OK, hopefully the problems we've had on our mirrors should be resolved
now. Please do let me know if not, and preferably any errors and your
rough geographical location.

Thanks for your patience!

Dan.


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Re: [biomart-users] Re: Error in getBM

francisca.rojas.r
Hi Dan,

Now it's working fine again.
Just so you know, my location is Baltimore MD, and I had tried using other hosts (www.ensembl.org, uswest.ensembl.org) bu they gave me the same error.
But everything is fine now!

Thank you for your help.

Kind regards,

Francisca

On Friday, September 23, 2016 at 9:57:57 AM UTC-4, Dan Staines (EBI) wrote:
OK, hopefully the problems we've had on our mirrors should be resolved
now. Please do let me know if not, and preferably any errors and your
rough geographical location.

Thanks for your patience!

Dan.


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