Hi
Reporting this biomaRt error which has been occurring recurrently over the last week
biomaRt error :: The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.
All attributes appear valid. I have also tried subsetting on a smaller number of attributes without success.
Advice, input and resolution welcome.
Cheers. Ashley
> library(biomaRt)
> listMarts(host="www.ensembl.org")
> human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", host="www.ensembl.org")
> listAttributes(human)
> attributes = c("ensembl_gene_id", "hgnc_symbol", "mmusculus_homolog_ensembl_gene", "mmusculus_homolog_associated_gene_name", "mmusculus_homolog_perc_id_r1")
> listFilters(human, what = c("name", "description"))
> orth.mouse = getBM(attributes,filters="with_mmusculus_homolog",values=TRUE, mart = human,uniqueRows=TRUE)
<!DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN>
1 <html><head>
2 <title>302 Found</title>
3 </head><body>
4 <h1>Found</h1>
5 <p>The document has moved <a href=//asia.ensembl.org/biomart/martservice?;redirectsrc=//www.ensembl.org%2Fbiomart%2Fmartservice%3F>here</a>.</p>
6 </body></html>
Error in getBM(attributes, filters = "with_mmusculus_homolog", values = TRUE, :
The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.32.1 BiocInstaller_1.26.1 edgeR_3.18.1 AnnotationDbi_1.38.2 IRanges_2.10.5
[6] S4Vectors_0.14.7 Biobase_2.36.2 BiocGenerics_0.22.1 limma_3.32.10
I have made some more updates to biomaRt, available in version 2.35.4 (
BiocInstaller::biocLite('grimbough/biomaRt')), hopefully this fixes things.Since this seems to be affecting a lot of people, it would be really helpful if anyone experiencing the problem could provide a small example, along with their location the world. You can do this at this Github issue (https://github.com/grimbough/biomaRt/issues/1)
I'm also in discussion with the Ensembl team to determine the best way forward in the future.