Question

BioMart webservice returned an invalid result

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mcall ▴ 20

@mcall-11507

Last seen 4.8 years ago

Hi!

Since yesterday I'm trying to annotate based on Ensembl ids, however, in some cases it works, but the majority of the times that I try, I receive the following error:

Batch submitting query [=================================================================================>------] 94% eta: 49sError in getBM(attributes = columns, filters = keytype, values = keys, : 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

What else should I send?

Many thanks,

Maria

software error annotation BioMart • 585 views

ADD COMMENT • link updated 5.5 years ago by Mike Smith ★ 6.6k • written 5.5 years ago by mcall ▴ 20

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You should also send the code that preceded that call, and better yet a self-contained example that anybody can run to replicate the error. In addition, the output from running sessionInfo.

ADD REPLY • link 5.5 years ago James W. MacDonald 67k

score 0 · Answer 1 · 2019-06-21

It might be that the main Ensembl site is being a bit slow today. You can try querying one of the mirror sites e.g.

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

Values for the mirror argument are: useast, uswest, asia. You'll need to modified the dataset argument if you're not accessing human genes.