getBM error: The query to the BioMart webservice returned an invalid result
1
3
Entering edit mode
Gregulator ▴ 30
@gregulator-9309
Last seen 21 months ago
Australia

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 • 4.8k views
ADD COMMENT
4
Entering edit mode
Mike Smith ★ 5.1k
@mike-smith
Last seen 5 hours ago
EMBL Heidelberg / de.NBI

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 COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 221 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6