Question: BioMart : Error in getBM, the BioMart webservice returned an invalid result
2
gravatar for amandinelecerfdefer
4 months ago by
amandinelecerfdefer20 wrote:

Hello,

Thanks to a file containing a list of rsIDs, I want to retrieve the name of the gene and transcripts corresponding to each rsID. tool :

install.packages('BiocManager', repos='http://cran.us.r-project.org')
BiocManager::install(c("biomaRt"))

library(biomaRt)
Data <- read.delim("/Users/amandinelecerfdefer/Desktop/Modification_vcf/cut/rsID_origine.txt2.txt")

snpmart <-
  useMart(biomart = "ENSEMBL_MART_SNP", dataset = "hsapiens_snp")
T1<-Sys.time()
T1
res <- getBM(
  attributes = c(
    "refsnp_id",
    "ensembl_gene_stable_id",
    "ensembl_transcript_stable_id"
  ),
  filters = "snp_filter",
  values = Data$rsID,
  mart = snpmart,
  uniqueRows = TRUE
)

T2<-Sys.time()
T2
write.csv(res, file = "/Users/amandinelecerfdefer/Desktop/Modification_vcf/name_cut/recovery_gene_trans_original2.txt")
Tdiff= difftime(T2, T1) 
Tdiff
write.csv(Tdiff, file = "/Users/amandinelecerfdefer/Desktop/Modification_vcf/time/time2.txt")`enter code here`

Last week this tool worked very well but for a few days now, it has been impossible to launch it due to a recurring error.

I have this error :

> res <- getBM(
+   attributes = c(
+     "refsnp_id",
+     "ensembl_gene_stable_id",
+     "ensembl_transcript_stable_id"
+   ),
+   filters = "snp_filter",
+   values = Data$rsID,
+   mart = snpmart,
+   uniqueRows = TRUE
+ )
Batch submitting query [=======>-----------------------------------------------------]  13% eta:  2hError in getBM(attributes = c("refsnp_id", "ensembl_gene_stable_id", "ensembl_transcript_stable_id"),  : 
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. 
Please report this on the support site at http://support.bioconductor.org

How to fix this error and make the tool work?

biomart getbm webservice • 166 views
ADD COMMENTlink modified 4 months ago by Mike Smith4.0k • written 4 months ago by amandinelecerfdefer20

I encountered the exact same error this morning.

ADD REPLYlink written 4 months ago by zhuo0

Received same error couple hours back today.

ADD REPLYlink written 4 months ago by GENOMIC_region0
Answer: BioMart : Error in getBM, the BioMart webservice returned an invalid result
1
gravatar for Mike Smith
4 months ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

The main Ensembl site seems to have been quite slow for the past week or so. You can try querying one of the Ensembl mirrors which may be more responsive for you e.g.

mart <- useEnsembl(biomart = "ensembl", 
                   dataset = "hsapiens_snp", 
                   mirror = "useast")

Values for the mirror argument are: useast, uswest, asia

ADD COMMENTlink modified 4 months ago • written 4 months ago by Mike Smith4.0k

Thank you. I take note of your answer and I try it. Thank you

ADD REPLYlink written 4 months ago by amandinelecerfdefer20
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