Error in biomaRt::getBM(attributes = c("ensembl_transcript_id", "external_gene_name")
1
0
Entering edit mode
e.everman • 0
@eeverman-14774
Last seen 2.1 years ago
United States

This suddenly stopped working after functioning for several weeks without issue:

ensemble = useMart("ENSEMBL_MART_ENSEMBL")
map_mart <- biomaRt::useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL", 
                             dataset = "dmelanogaster_gene_ensembl", 
                             host = "www.ensembl.org")              

t2g <- biomaRt::getBM(attributes=c("ensembl_transcript_id","external_gene_name"), mart = map_mart)  

But, now throws the following error after running the last line:

Error in biomaRt::getBM(attributes = c("ensembl_transcript_id", "external_gene_name"),  : 
  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

I'm not sure what the source of the problem is, any direction would be appreciated.

Versions: biomaRt: 2.4.3 R session info:

R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] preprocessCore_1.46.0 biomaRt_2.40.3        sleuth_0.30.0        
 [4] Rmisc_1.5             plyr_1.8.5            lattice_0.20-38      
 [7] forcats_0.4.0         stringr_1.4.0         dplyr_0.8.3          
[10] purrr_0.3.3           readr_1.3.1           tidyr_1.0.0          
[13] tibble_2.1.3          ggplot2_3.2.1         tidyverse_1.3.0      

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3           lubridate_1.7.4      prettyunits_1.0.2   
 [4] assertthat_0.2.1     zeallot_0.1.0        digest_0.6.23       
 [7] R6_2.4.1             cellranger_1.1.0     backports_1.1.5     
[10] reprex_0.3.0         stats4_3.6.2         RSQLite_2.1.2       
[13] httr_1.4.1           pillar_1.4.3         progress_1.2.2      
[16] rlang_0.4.2          curl_4.3             lazyeval_0.2.2      
[19] readxl_1.3.1         rstudioapi_0.10      data.table_1.12.2   
[22] blob_1.2.0           S4Vectors_0.22.0     RCurl_1.95-4.12     
[25] bit_1.1-14           munsell_0.5.0        broom_0.5.2         
[28] compiler_3.6.2       modelr_0.1.5         pkgconfig_2.0.3     
[31] BiocGenerics_0.30.0  tidyselect_0.2.5     IRanges_2.18.1      
[34] XML_3.98-1.20        fansi_0.4.1          crayon_1.3.4        
[37] dbplyr_1.4.2         withr_2.1.2          bitops_1.0-6        
[40] grid_3.6.2           nlme_3.1-142         jsonlite_1.6        
[43] gtable_0.3.0         lifecycle_0.1.0      DBI_1.1.0           
[46] magrittr_1.5         scales_1.1.0         cli_2.0.1           
[49] stringi_1.4.5        fs_1.3.1             xml2_1.2.2          
[52] generics_0.0.2       vctrs_0.2.1          Rhdf5lib_1.6.0      
[55] tools_3.6.2          bit64_0.9-7          Biobase_2.44.0      
[58] glue_1.3.1           hms_0.5.3            parallel_3.6.2      
[61] AnnotationDbi_1.46.0 colorspace_1.4-1     rhdf5_2.28.0        
[64] rvest_0.3.5          memoise_1.1.0        haven_2.2.0  
software error biomaRt • 749 views
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2
Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 3 hours ago
EMBL Heidelberg

This usually indicates some instability with the main Ensembl webserver. You can try querying one of the mirrors e.g.

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

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

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0
Entering edit mode

Thanks for the help. I figured that had to be what was going on. Both work this morning. I'll keep this in mind for the future!

Cheers, Elizabeth

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