Question: getBM error: The query to the BioMart webservice returned an invalid result
3
gravatar for Gregulator
19 months ago by
Gregulator30
Australia
Gregulator30 wrote:

Hey.

I get this error everytime I use getBM() function:

"The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list."

I had this same problem last time BiomaRt released an update but it was fixed by installing latest version. Not working this time. Am I doing something stupid?

Here is a full list of my commands and session info:

>  mart<-useMart("ENSEMBL_MART_ENSEMBL", "mmusculus_gene_ensembl")
> ensembl.ids <- c(mydataset$Ensembl_ID)

> head(ensembl.ids)
[1] "ENSMUSG00000000001" "ENSMUSG00000000028" "ENSMUSG00000000031" "ENSMUSG00000000037"
[5] "ENSMUSG00000000049" "ENSMUSG00000000056"

> ensembl.entrez.retrieve<-getBM(attributes=c('mgi_symbol', 'ensembl_gene_id', 'entrezgene', "refseq_mrna"), filters = 'ensembl_gene_id', values = ensembl.ids, mart = mart)
Error in getBM(attributes = c("mgi_symbol", "ensembl_gene_id", "entrezgene",  : 
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] car_2.1-6       lattice_0.20-35 biomaRt_2.34.2  edgeR_3.20.8    limma_3.34.7   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15         nloptr_1.0.4         pillar_1.1.0         compiler_3.4.3      
 [5] prettyunits_1.0.2    bitops_1.0-6         tools_3.4.3          progress_1.1.2      
 [9] lme4_1.1-15          digest_0.6.15        bit_1.1-12           nlme_3.1-131        
[13] RSQLite_2.0          memoise_1.1.0        tibble_1.4.2         mgcv_1.8-23         
[17] rlang_0.1.6          Matrix_1.2-12        DBI_0.7              curl_3.1            
[21] yaml_2.1.16          parallel_3.4.3       SparseM_1.77         xml2_1.2.0          
[25] stringr_1.2.0        httr_1.3.1           MatrixModels_0.4-1   S4Vectors_0.16.0    
[29] IRanges_2.12.0       locfit_1.5-9.1       stats4_3.4.3         bit64_0.9-7         
[33] grid_3.4.3           nnet_7.3-12          Biobase_2.38.0       R6_2.2.2            
[37] AnnotationDbi_1.40.0 XML_3.98-1.9         minqa_1.2.4          blob_1.1.0          
[41] magrittr_1.5         splines_3.4.3        BiocGenerics_0.24.0  MASS_7.3-48         
[45] assertthat_0.2.0     pbkrtest_0.4-7       quantreg_5.34        stringi_1.1.6       
[49] RCurl_1.95-4.10  

 

biomart • 3.0k views
ADD COMMENTlink modified 19 months ago by Mike Smith3.9k • written 19 months ago by Gregulator30
Answer: getBM error: The query to the BioMart webservice returned an invalid result
4
gravatar for Mike Smith
19 months ago by
Mike Smith3.9k
EMBL Heidelberg / de.NBI
Mike Smith3.9k wrote:

Since you're in Australia, you're being redirected to the asian Ensembl mirror, which looks like it's down at the moment (https://asia.ensembl.org/index.html?redirect=no).

You can force using the main Ensembl site using:

mart<-useMart(biomart = "ENSEMBL_MART_ENSEMBL", 
              dataset = "mmusculus_gene_ensembl", 
              host = "www.ensembl.org",
              ensemblRedirect = FALSE)

This seems to be happening a lot at the moment, so I'll try and put a more informative error message in place.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Mike Smith3.9k

Mate, you're a legend. Should have checked that myself. working fine now

ADD REPLYlink written 19 months ago by Gregulator30
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