BioMart: connection fails
2
2
Entering edit mode
3.2 years ago
salamandra ▴ 410

Hi,

running this

ensembl = useMart(biomart ="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="may2017.archive.ensembl.org")

or this:

ensembl = useMart(biomart ="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="http://dec2017.archive.ensembl.org")

used to work in the past. but now it gives the error:

Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check http://www.biomart.org and verify if this website is available. Error: XML content does not seem to be XML:

The site is up, the internet connection also. In the site it says this:

If you are a user of biomaRt (a part of the Bioconductor library) change the host from 'www.biomart.org' to 'www.ensembl.org'

But in the commands I used to run there's no 'www.biomart.org' to replace...

Do you know what is the correct command now?

I also tried:

ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="www.ensembl.org")

and didn't work

BioMart • 4.7k views
0
Entering edit mode

Hi, now it's not working again. With

useast.ensembl.org

uswest.ensembl.org

and even if I run:

listMarts()

get the error:

 Request to BioMart web service failed. The BioMart web service you're
accessing may be down. Check the following URL and see if this website
is available:
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Error in if (!grepl(x = registry, pattern = "^\n*<MartRegistry>")) { :
argument is of length zero


Since Friday I've been trying. It doesn't seem the link they ask to follow is working, but the link suggested by Mike Smith: http://www.ensembl.org/biomart/martview?redirect=no is woking.

Besides, when using ensemblRedirect = F I get the aditional warning:

In addition: Warning message:
In useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl",  :
The argument "ensemblRedirect" has been deprecated and will be removed in the next biomaRt release.


Should I just wait some more days or is there another way around?

R version is 3.5.1

0
Entering edit mode
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt


redirects to

http://uswest.ensembl.org/biomart/martservice?type=registry&requestid=biomaRt


and generates this. So seems to be ok.

<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>

0
Entering edit mode

Yes, from the links seems to be working and when I was one other computer (mac) it doesn't give an error, but when I use this computer (windows) it doesn't work. Could be some problem with package version? I tried to install same package version on both without success.

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Entering edit mode

If you're using the same package version then there shouldn't be any difference between which operating system you're using. However the code has change quite a bit across the last ver versions, so I would make sure you are using the latest version (2.38.0) and R 3.5.

6
Entering edit mode
3.2 years ago
Mike Smith ★ 1.7k

As Emily has said, parts of Ensembl are down right now. This includes the archive sites and the BioMart interface at the main site. You can check this just by visiting in a browser (http://www.ensembl.org/biomart/martview?redirect=no) - at the moment you get an error page.

However you can use one of the mirror sites e.g. http://uswest.ensembl.org/biomart/martview?redirect=no

To do this using the biomaRt package you would do something like:

ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL",
dataset="hsapiens_gene_ensembl",
host="uswest.ensembl.org",
ensemblRedirect = FALSE)


I would also suggest updating your version of biomaRt (and maybe also R). The error message about visiting www.biomart.org is misleading and is no longer produced in more recent versions of biomaRt. You now get a more appropriate URL to try, that would have taken you to the error page at Ensembl.

2
Entering edit mode

Since I often land on this answer (by the will of Google), whenever I look through my colleague's older scripts, I'll pin the following newer answer to this answer: https://support.bioconductor.org/p/134617/

0
Entering edit mode

thanks! had also to change the R version in order to work

0
Entering edit mode

Hi, now it's not working again. With

useast.ensembl.org

uswest.ensembl.org

and even if I run:

listMarts()


get the error:

Request to BioMart web service failed. The BioMart web service you're
accessing may be down. Check the following URL and see if this website
is available:
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Error in if (!grepl(x = registry, pattern = "^\n*<MartRegistry>")) { :
argument is of length zero


Since Friday I've been trying. It doesn't seem the link they ask to follow is working, but the link suggested by Mike Smith: http://www.ensembl.org/biomart/martview?redirect=no is woking.

Besides, when using

ensemblRedirect = F

In addition: Warning message:
In useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl",  :
The argument "ensemblRedirect" has been deprecated and will be removed in the next biomaRt release.


Should I just wait some more days or is there another way around?

R version is 3.5.1

4
Entering edit mode
3.2 years ago

The archive sites are currently down due to disk problems. We're currently working on getting them fixed.

0
Entering edit mode

ok, could you then please tell how is the command to access the current version instead of the archives?

1
Entering edit mode

Try useast.ensembl.org or uswest.ensembl.org. It is possible that though @Emily referred to archive sites being down, even the current BioMarts could be down as well.

0
Entering edit mode

Archives are now back.