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ldetorrente
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@ldetorrente-10730
Last seen 7.9 years ago
Dear all,
I am using biomaRt for a long time to map ENSEMBL ID to Gene symbol but since this morning I am getting an error and cannot make it work anymore. It's exactly the same script I was using yesterday and when I try it on another machine it works.
Thank you for your help!
> library(biomaRt)
> my_Ensembl=c("ENSG00000272449","ENSG00000272468","ENSG00000272520")
> mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
> Genes=getBM(attributes=c("ensembl_gene_id","hgnc_symbol"),filters="ensembl_gene_id",values=my_Ensembl,mart=mart)
Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"), filters = "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.
> sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.5 (Yosemite) 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] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.26.1 loaded via a namespace (and not attached): [1] IRanges_2.4.8 parallel_3.2.3 DBI_0.5-1 [4] RCurl_1.95-4.8 Biobase_2.30.0 AnnotationDbi_1.32.3 [7] RSQLite_1.0.0 S4Vectors_0.8.11 BiocGenerics_0.16.1 [10] stats4_3.2.3 bitops_1.0-6 XML_3.98-1.4
+1
Just came across the same issue tonight. Script I've been using for a few months suddenly not working.
I tried pointing useMart to a different mirror, but same error.
Currently updating my Bioconductor libraries to see if this fixes the issue. Will post solution when I come across one.
I tried to change the host to www.ensembl.org and it didn't change anything. I was first trying from work and when I came back home I tried again a few hours ago and it was working (same laptop). The weird thing is that I ran my script just now and it's not working again with the same error.
It has to be an issue with the primary mirrors. The following works:
mart <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host = "jul2016.archive.ensembl.org");
res <- getBM(attributes=c("external_gene_name","ensembl_gene_id","description"), values=my_Ensembl, mart=mart);
Is this still proving an issue? Everything seems to be working fine for me across several mirrors, using both the versions of R & biomaRt you're using, and the most up-to-date. The error message very much looks like something server side though.
Yes, everything does seem fine right now though we're investigating to see if there was a problem yesterday. Will let you know what we find out.
Yes, it's working again now. I'll let you know if it happens again, Thanks!