Question

biomaRt: Unexpected format to the list of available marts.

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frank007 • 0

@frank007-19497

Last seen 4.2 years ago

The following command produces the error message mentioned below:

> mart = useMart("ensembl")

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

Referring to the help function everything should be okay if the URL within the eror message produces the following output:

<MartRegistry>
  <MartURLLocation database="ensembl_mart_95" default="1" displayName="Ensembl Genes 95" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_95" default="" displayName="Mouse strains 95" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_95" 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_95" 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_95" default="" displayName="Genomic features 95" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_95" default="" displayName="Ensembl Variation 95" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_95" default="" displayName="Ensembl Regulation 95" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>

I use version 2.36.1 . Any idea how to solve this issue?

Frank

software error biomaRt • 2.8k views

ADD COMMENT • link 5.3 years ago frank007 • 0

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This is odd, because you're getting the correct result in the browser, so it isn't a fundamental connection problem either at your end or with Ensembl. Your code also works fine for me.

You could try using one of the mirror sites e.g.

mart <- useEnsembl('ensembl', mirror = 'useast')

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

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The usage of another mirror (here: useast) works perfectly whereas the same command without a mentioned mirror on the same system still does not work. It is strange, but it solves at least the problem.

Thanks! Frank

ADD REPLY • link 5.3 years ago frank007 • 0

score 0 · Answer 1 · 2019-01-17

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frank007 • 0

@frank007-19497

Last seen 4.2 years ago

The problem is still not clear to me. You should follow the detailed description provided in the error message to perform some additional tests wrt. the connection. If it still does not work, you can try to switch to another mirror. That can solve the problem.

For example use: mart <- useEnsembl('ensembl', mirror = 'useast')

.... instead of: mart <- useEnsembl('ensembl')

ADD COMMENT • link 5.3 years ago frank007 • 0

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More often that not this error occurs when Ensembl is down for maintenance, and all requests get redirected to a status page. Thus you don't get any sort of HTTP error to detect, so asking a user to open the link is a quick way for them to determine what the issue is.

However, this clearly isn't the issue here. Out of interest, does this work for you?

mart <- useMart('ensembl', host = "https://www.ensembl.org/", port = 443)

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