BiomaRt: Query ERROR (database error)
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lucer105 • 0
@lucer105-11538
Last seen 7.7 years ago

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        

 

 

annotation biomart bioconductor • 1.4k views
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Dan Staines ▴ 70
@dan-staines-10687
Last seen 7.7 years ago
EMBL-EBI
can I ask what part of the world you're connecting from?
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I reproduced this error just now, from Buffalo, NY, 67.99.175.226

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the error message suggests its a mirror site that you've been directed to, and would guess useast. I'll pass this on to the folks who look after the mirrors - thanks for your patience...
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Query works again~ Thank you so much!

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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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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).

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