Question

Is biomaRt down?

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ben.run974 • 0

@benrun974-6879

Last seen 4.8 years ago

United Kingdom

Hi,

For the last few days I have been using biomaRt with no problem but since yesterday I keep getting error messages:

> getEnsemblID <- getBM(attributes = c('mgi_id', 'ensembl_gene_id'), filters = 'mgi_id', values = getGeneAnnot[, 1], mart = useMart(biomart = 'ensembl', dataset = 'mmusculus_gene_ensembl'),  verbose = T)
Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
  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

Is the service down?

Thanks for your help!

Ben

biomart • 2.3k views

ADD COMMENT • link updated 13 months ago by Xinling • 0 • written 5.3 years ago by ben.run974 • 0

score 0 · Answer 1 · 2019-01-08

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Mike Smith ★ 6.5k

@mike-smith

Last seen 8 hours ago

EMBL Heidelberg

Did you try visiting the page suggested in the error message? Did it go anywhere, or time out?

The main Ensembl site seemed to be very slow yesterday. There are several mirror that you can try using if the main site isn't working. You can elect to use these with:

mart <- useEnsembl(biomart = 'ensembl', 
                   dataset = 'mmusculus_gene_ensembl',
                   mirror = 'uswest')
getEnsemblID <- getBM(attributes = c('mgi_id', 'ensembl_gene_id'), 
                      filters = 'mgi_id', 
                      values = getGeneAnnot[, 1], 
                      mart = mart, 
                      verbose = T)

The possible values for the mirror argument are uswest, useast and asia.

ADD COMMENT • link 5.3 years ago Mike Smith ★ 6.5k

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Hi Mike,

Thanks for your help!

I did try to go on the suggested page and I got that:

<MartRegistry>
  <MartURLLocation database="ensembl_mart_94" default="1" displayName="Ensembl Genes 94" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_94" default="" displayName="Mouse strains 94" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_94" default="" displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_94" default="" displayName="Ontology" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_94" default="" displayName="Genomic features 94" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_94" default="" displayName="Ensembl Variation 94" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_94" default="" displayName="Ensembl Regulation 94" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>

That's being said it seems to work again (both BiomaRt and main website). Next time I will bump into that issue I will try to use different mirror.

Thanks again.

Ben

ADD REPLY • link 5.3 years ago ben.run974 • 0

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Dear Ben,

We released our newest version of Ensembl (e!95) on Wednesday so this might be why you experienced some issues. Please let me know if you still have problems with our marts.

Apologies for any inconvenience caused. Kind Regards, Thomas

ADD REPLY • link 5.3 years ago Thomas Maurel ▴ 800

score 0 · Answer 2 · 2023-02-22

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Xinling • 0

@68cc3742

Last seen 13 months ago

United States

Is biomart down? When I clicked https://useast.ensembl.org/info/data/biomart/index.html I got the error saying 504 gateway time-out.