Got error message when running biomart query. Could anyone help? I also ran the same query on ensembl website, got same error message..... You help is appreciated~
library("biomaRt") ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="xmaculatus_gene_ensembl", host="www.ensembl.org") test<-c("ENSXMAT00000014060", "ENSXMAT00000012103", "ENSXMAT00000018270", "ENSXMAT00000020151", "ENSXMAT00000008275", "ENSXMAT00000016765") getBM( c("ensembl_gene_id","external_gene_name"), "ensembl_transcript_id", test, mart=ensembl)
Error in getBM(c("ensembl_gene_id", "external_gene_name"), "ensembl_transcript_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 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
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_2.22.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.28.2 Biobase_2.26.0 BiocGenerics_0.12.1 bitops_1.0-6 DBI_0.3.1 GenomeInfoDb_1.2.5 IRanges_2.0.1 parallel_3.1.2 RCurl_1.95-4.7
[10] RSQLite_1.0.0 S4Vectors_0.4.0 stats4_3.1.2 XML_3.98-1.3
I reproduced this error just now, from Buffalo, NY, 67.99.175.226
Query works again~ Thank you so much!
I am near Austin, TX. This error message has been there for the 3rd day for me (not sure how long it has been there).