This is a test version of Biostars. For the public version, visit https://www.biostars.org.
biomaRt GRCh37 down?

Hi, I am currently getting the following error:

library(biomaRt)

mart<-useMart(biomart="ENSEMBL_MART_ENSEMBL",
              dataset="hsapiens_gene_ensembl", 
              host="grch37.ensembl.org")

Extra content at the end of the document
Error: 1: Extra content at the end of the document

I can't find any post specifying any scheduled maintenance. Is the server down?

Thanks!

biomart r ensembl grch37.enesmbl.org
• 3,308 views • link
updated by Ben Moore Ben Moore • written by alexander.nash • alexander.nash

I am also getting the same error.

Any info about maintenance?

• 0 views • link
written by edgarjavi • edgarjavi

1 answer

Hello,

There was a temporary disruption with the servers at the time you experienced this error message yesterday. Everything is running as it should be now. If you encounter any further errors (or are still encountering the same problem), please e-mail helpdesk@ensembl.org, and we will be able to assist you from there.

Best wishes

Ben Ensembl Helpdesk

• 0 views • link
written by Ben Moore Ben Moore

Log in to answer this question.

More posts like this
  • GATK GRCh38 genome version for biomaRt
    written by ramiro.barrantes • ramiro.barrantes
    Hello, I am using iGenomes GATK.GRCh38 with sarek. Now I need to use the R package biomaRt to fetch the sequence and other information. What …
  • map Ensembl gene ID from hg19 to hg38
    written by pingu77 • pingu77
    Hello! I would like to convert Ensembl gene ID from hg19 to hg38 with R. I tried with this code: ```r ensembl <- useMart("ensembl", dataset …
  • Can´t acces Biomart via R anymore
    written by Beginner • Beginner
    Hi, my R code previously accessed Biomart via: library("biomaRt") mart=useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", host="www.ensembl.org") resMArt=getBM(attributes=c("ensembl_gene_id","description","mgi_symbol"),mart=mart) resMArt2=getBM(attributes=c("ensembl_gene_id","gene_biotype"),mart=mart) however, mart=useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", host="www.ensembl.org") now gives the error: Error in listMarts(host …
  • biomaRt: Timeout on getBM().
    written by lincaijin1994 • lincaijin1994
    Hi. I want to get the exon annotation of a list of chromosome interval (hg19). Here is the code: getBM_value <- list( chromosome_name = bed_df$chromosome_name, …
  • dbSNP build in ENSEMBL biomaRt?
    written by 09meh • 09meh
    I'm wondering how to determine what dbSNP build (i.e. 150 or 151) the variation annotations are based on. For example, I can find that for …
  • Transcript biotypes for ncRNA in GRCh37 using biomaRt?
    written by Sergio Martínez Cuesta Sergio Martínez Cuesta
    Dear all, I am attempting to retrieve transcript biotypes for ncRNAs using Bioconductors's biomaRt in GRCh37 as follows: library(biomaRt) ensembl <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", dataset="hsapiens_gene_ensembl") # …
  • BioMart: connection fails
    written by salamandra salamandra
    Hi, running this > ensembl = useMart(biomart > ="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="may2017.archive.ensembl.org") or this: > ensembl = useMart(biomart > ="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="http://dec2017.archive.ensembl.org") used to work in the past. …
  • Map ensembl gene id form hg38 in hg19
    written by Tanvir Ahamed Tanvir Ahamed
    I want to map all ensembl gene id form hg38 in hg19. Any help will be appreciated ? Thanks !! # Example : Loading library …
  • Ensembl biomaRt Down?
    written by andrew.j.skelton73 andrew.j.skelton73
    Hi, Currently getting the following error: library(biomaRt) ensembl <- useMart("ensembl") Extra content at the end of the document Error: 1: Extra content at the end …
  • biomaRt GRCh37 down?
    written by andrew.j.skelton73 andrew.j.skelton73
    Hi, Using the connection string: ``` grch37 <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "grch37.ensembl.org", path = "/biomart/martservice", dataset = "hsapiens_gene_ensembl") ``` Doesn't appear to work, …