Question

Ensembl biomaRt connection errors

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genomicsio • 0

@genomicsio-10961

Last seen 7.7 years ago

require("biomaRt") 
human <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org" )
# Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets function.

human <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org" )
#Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Entity 'nbsp' not defined Error: 1: Space required after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing 4: Entity 'nbsp' not defined 

#[repeat 5 times with same error] 
human <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org" ) 
human 
#Object of class 'Mart': Using the ENSEMBL_MART_ENSEMBL BioMart database Using the dataset 

datasets <- listDatasets(mart)
datasets[grep("hsapiens", datasets$dataset),] 
#dataset                    description   version
#32 hsapiens_gene_ensembl Homo sapiens genes (GRCh38.p5) GRCh38.p5

human <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org" ) 
# Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : The given dataset: hsapiens_gene_ensembl, is not valid. Correct dataset names can be obtained with the listDatasets function. 

# let's try the Asia mirror 
human <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "asia.ensembl.org" ) 
#Error in bmAttrFilt("filters", mart, verbose = verbose) : biomaRt error: looks like we're connecting to incompatible version of BioMart suite.

software error biomart ensembl • 5.1k views

ADD COMMENT • link updated 8.4 years ago by Dan Staines ▴ 70 • written 8.4 years ago by genomicsio • 0

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Sorry for the terrible formatting...

ADD REPLY • link 8.4 years ago genomicsio • 0

score 0 · Answer 1 · 2016-06-23

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Dan Staines ▴ 70

@dan-staines-10687

Last seen 8.2 years ago

EMBL-EBI

Sorry to hear you're having problems! Can you confirm when you see this problem, and if its a continual problem or intermittent? Many thanks, Dan.

ADD COMMENT • link 8.4 years ago Dan Staines ▴ 70

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I am also having this problem with biomaRt. It seems like a hit and miss process as to whether you get a connection or not. Two days ago within the space of an hour I was getting connection some of the time and all worked as normal. But also within that hour there were many times when I just wasn't getting a connection and I was getting error messages. I was trying both the default ensembl site and the asian mirror.

I am not getting a connection now.

> library("biomaRt")
> mouse<-useMart(host="www.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl")
Error in useMart(host = "www.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl") :
Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
> mouse<-useMart(host="asia.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl")
Error in useMart(host = "asia.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl") :
Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
> listMarts(host="www.ensembl.org")
[1] biomart version
<0 rows> (or 0-length row.names)
> listMarts(host="asia.ensembl.org", verbose = TRUE)
Attempting web service request:
http://asia.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
[1] biomart version
<0 rows> (or 0-length row.names)

ADD REPLY • link 8.4 years ago s.corley ▴ 30

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It looks like our Asia biomart mirror is currently down. We'll look into restarting this ASAP. Other problems may reflect excessive load on the BioMart servers, particularly by queries using very large numbers of regions or IDs. We're currently investigating how we might handle this.

ADD REPLY • link 8.4 years ago Dan Staines ▴ 70

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It seems like there is a persistent problem with accessing the biomart service...

I saw the earlier Tweet that Ensembl servers were handling excessive queries, but I guess this situation has not changed.

> listMarts(host = "www.ensembl.org", verbose = T) Attempting web service request: http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt [1] biomart version <0 rows> (or 0-length row.names) > listMarts(host = "asia.ensembl.org", verbose = T) Attempting web service request: http://asia.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt [1] biomart version <0 rows> (or 0-length row.names)

ADD REPLY • link 8.4 years ago genomicsio • 0