Question

Something wrong with the BioMart server

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Dan Liang • 0

@dan-liang-20865

Last seen 5.5 years ago

Hi,

I got an error when I tried to call genes suing bioMart.

genemart = useMart(biomart="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl");
Error in listMarts() : Unexpected format to the list of available marts.

Please check the following URL manually, and try ?listMarts for advice. http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt

Then I checked the link, it is the right list, so I think there is something wrong with the BioMart server. Hope this is the right way to report this error. Very appreciate it if you could fix it.

Thanks!

Dan

bioMart • 8.2k views

ADD COMMENT • link updated 5.5 years ago by Mike Smith ★ 6.6k • written 5.5 years ago by Dan Liang • 0

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Same thing here:

ensembl = useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl") Error in bmRequest(request = request, ssl.verifypeer = ssl.verifypeer, : Not Found (HTTP 404).

ADD REPLY • link 5.5 years ago psbpedrobarbosa ▴ 10

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Same thing here:

ensembl = useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl") Error in bmRequest(request = request, ssl.verifypeer = ssl.verifypeer, : Not Found (HTTP 404).

ADD REPLY • link 5.5 years ago psbpedrobarbosa ▴ 10

score 2 · Answer 1 · 2019-05-23

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Mike Smith ★ 6.6k

@mike-smith

Last seen 8 hours ago

EMBL Heidelberg

I currently get an error when I visit the main Ensembl site. You can try querying one of the mirrors e.g.

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

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

ADD COMMENT • link 5.5 years ago Mike Smith ★ 6.6k

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That works! Thanks!

ADD REPLY • link 5.5 years ago Dan Liang • 0