News:Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016

Question

[Ben Moore]

The Sanger datacentre, which hosts most Ensembl resources in the UK, will be shutting down from the afternoon (BST) of Friday 26th August until the afternoon of Tuesday 30th August 2016 for essential maintenance. This will impact Ensembl services and we apologise for any inconvenience.

The following websites will be unavailable between 1230 GMT (UTC) on Friday 26th August and approximately 1300 GMT on Tuesday 30th August:

• www.ensembl.org
• grch37.ensembl.org
• The archive websites (such as http://dec2015.archive.ensembl.org/)
• Vega and Pre!

You will still be able to access Ensembl using one of our mirror sites, such as useast.ensembl.org, uswest.ensembl.org or asia.ensembl.org. Logins and Tools (such as the VEP or BLAST) will not be available on the mirror sites during this period. Note that the mirrors only provide access to our latest version (ie Ensembl 85), so there will be no way to access either the archives or GRCh37.

Ensembl Genomes, encompassing bacteria.ensembl.org, plants.ensembl.org, fungi.ensembl.org, protists.ensembl.org and metazoa.ensembl.org, will all be functional.

The public MySQL database servers

The public database servers at ensembldb.ensembl.org and martdb.ensembl.org will also be affected during this period and will therefore be inaccessible via either the Perl API or direct MySQL queries. The mirror databases useastdb.ensembl.org and asiadb.ensembl.org will be accessible using ports 3306 and 5306, as usual. If you are running any pipelines that use the Hinxton database servers we recommend that you stop them before the shut-down, or that you reconfigure them to use one of the mirror databases.

The Ensembl Genomes database at mysql-eg-publicsql.ebi.ac.uk, port 4157, will not be accessible via either the Perl API or direct MySQL access.

The Ensembl and Ensembl Genomes FTP sites will both be down. There is no alternative way to access the files on the FTP sites.

The REST servers

The REST API servers, including that for GRCh37, will be available.

Getting help

Ensembl helpdesk and the dev mailing list will both be closed. All emails will be held in a queue and dealt with when they are back up, although there may be some delay once we are set up again. You will receive no confirmation that your query has been sent until the systems are back up.

We will be monitoring BioStars for Ensembl questions, just tag with “Ensembl” to make sure we see it. We will also be available for short questions via Twitter and Facebook.

Answer 1

[deepue]

Is there any option of using Ensembl through biomaRt package ? At the moment, I am not able to access the marts.

[Ben Moore]

Yes, you can still access the mirror databases useastdb.ensembl.org and asiadb.ensembl.org using biomaRt (ports 3306 and 5306), as usual.

[Cumol]

Does not seem to work for me using this:

library(biomaRt)

listMarts(host = "asiadb.ensembl.org", port = 5306)

I get 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:

[Ben Moore]

We have had some reports of problems with BioMart on our mirrors as well, but we are hoping to resolve these issues quickly.

I'll re-comment when we have resolved this issue, letting you know you can try again.

[Ben Moore]

We hope this problem is now fixed. Please re-try to connect to one of the mirrors as before, and let us know whether you have any more problems.

[enricoferrero]

Still having issues here:

> ensembl <- useMart("ensembl", "hsapiens_gene_ensembl", host="useastdb.ensembl.org", port=3306)
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:

Answer 2

[Ben Moore]

The problem with the mirror access here is that the URL should not have 'db' in the name. It should just read 'uswest.ensembl.org', 'useast.ensembl.org' or 'asia.ensembl.org'.

[deepue]

Hi, I am still facing the issue

> listMarts()
Extra content at the end of the document
Error: 1: Extra content at the end of the document

Answer 3

[Ben Moore]

We're sorry to hear that you're still having problems- we're not entirely sure why you are not able to connect via the mirrors, as we have been able to replicate your error. Normal access will be restored on Tuesday 30th August. Sorry for any disruption caused.

[enricoferrero]

All right, no worries - I can wait till Tuesday ;)

[GenoMax]

Web access to BioMart appears to be working fine the US.

[deepue]

@Ben are you still looking into the issue ? Though it is around one day for the normal access, it will be useful to follow the workaround during future outages.

[enricoferrero]

Just to report I'm still getting errors using biomaRt through R, with both the main server and a mirror:

> ensembl <- useMart("ensembl", "hsapiens_gene_ensembl")
Extra content at the end of the document
Error: 1: Extra content at the end of the document
> ensembl <- useMart("ensembl", "hsapiens_gene_ensembl", host="useastdb.ensembl.org", port=3306)
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: