Question

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

2

Entering edit mode

ang ▴ 20

@ang-14621

Last seen 5.4 years ago

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

biomart number of columns in the result table does not equal the number of attributes in the query • 2.9k views

ADD COMMENT • link updated 6.4 years ago by thokall ▴ 160 • written 6.4 years ago by ang ▴ 20

1

Entering edit mode

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.

ADD REPLY • link 6.4 years ago Mike Smith ★ 6.5k

score 3 · Answer 1 · 2017-12-14

There appear to some issues with the release of ensembl ver. 91 some days ago perhaps your problem is related to this. See for example: C: biomaRt: drerio_gene_ensembl dataset missing

So try to to either install a patched version via GitHub

BiocInstaller::biocLite('grimbough/biomaRt')

and load the library again. Or consider using an older version of the ensembl data. The following will use version 90.

human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", "http://Aug2017.archive.ensembl.org")