BioMart : Error in getBM, the BioMart webservice returned an invalid result
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@amandinelecerfdefer-21004
Last seen 2.4 years ago

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 • 601 views
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I encountered the exact same error this morning.

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Received same error couple hours back today.

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Mike Smith ★ 5.2k
@mike-smith
Last seen 3 hours ago
EMBL Heidelberg / de.NBI

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

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0
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Thank you. I take note of your answer and I try it. Thank you

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