Question

Ensembl site unresponsive

1

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lirongrossmann ▴ 50

@lirongrossmann-23954

Last seen 3.8 years ago

Hi I have been trying to use the following code to get gene position via biomart :

ensembl_version="dec2016.archive.ensembl.org"
species="human"
ensembl = biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host=ensembl_version)

and received the following error:

Ensembl site unresponsive, trying www mirror
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Unknown cipher in list: DEFAULT@SECLEVEL=1

Does anyone else had similar issues? Few days ago I was able to run the same code with no issues.....

Thanks

ensembl biomart • 15k views

ADD COMMENT • link updated 3.6 years ago by tommaso.gastaldi • 0 • written 4.1 years ago by lirongrossmann ▴ 50

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I just visited ensembl.org and it looks like there's an issue

'The Ensembl web service you requested is temporarily unavailable. We are working to restore the service as soon as possible, and apologise for any inconvenience caused'

They've also got three mirrors of the Ensembl website listed if that helps.

ADD REPLY • link 4.1 years ago Terra • 0

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Can you include the output from sessionInfo() so we can see the package versions and operating system you're using?

ADD REPLY • link 4.1 years ago Mike Smith ★ 6.6k

score 2 · Answer 1 · 2020-10-12

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Mike Smith ★ 6.6k

@mike-smith

Last seen 15 hours ago

EMBL Heidelberg

The Ensembl site seems to have been undergoing some changes in the last few days, which have been affecting biomaRt access. I added some code to fix a problem with Ubuntu 20.04, and it looks like that broke 16.04, which I'm assuming you're using. The offending code should now only be run if it's needed, and hopefully it's fixed if you run BiocManager::install('grimbough/biomaRt') to get the latest version (2.45.7)

ADD COMMENT • link 4.1 years ago Mike Smith ★ 6.6k

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I installed it and I am still getting the same error....

Here is my session info: R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux

locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8
[5] LCMONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8 LCPAPER=enUS.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] biomaRt2.45.7 CONICSmat0.0.0.1

ADD REPLY • link 4.1 years ago lirongrossmann ▴ 50

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If you haven't done so already, can you make sure you close your R session, then restart and try running the biomaRt code again.

The setting that leads to the Unknown cipher in list: DEFAULT@SECLEVEL=1 error persists even after you've installed a new version of biomaRt, and is only cleared when R is re-started.

ADD REPLY • link 4.1 years ago Mike Smith ★ 6.6k

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Thanks! The connection has been established! but I get another error....

Here is my code:

ensembl_version="dec2016.archive.ensembl.org"
species="human"
gene_names <- row(matrix)
ensembl = biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host=ensembl_version)
gene_positions <- biomaRt::getBM(attributes=c('hgnc_symbol','chromosome_name','start_position','end_position'), filters ='hgnc_symbol', values =gene_names, mart = ensembl)

I get the following error:

Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery,  : 
  The query to the BioMart webservice returned an invalid result.
The number of columns in the result table does not equal the number of attributes in the query.
Please report this on the support site at http://support.bioconductor.org

It used to work without issues few days ago.....

ADD REPLY • link 4.1 years ago lirongrossmann ▴ 50

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You now have to explicitly use the https address of the site so:

ensembl_version = "https://dec2016.archive.ensembl.org"

ADD REPLY • link 4.1 years ago Mike Smith ★ 6.6k

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Hi, I have the same problem and used your suggestion:

ensembl <- useMart("https://dec2016.archive.ensembl.org", dataset="mmusculus_gene_ensembl")

Still anyway the error:

Ensembl site unresponsive, trying uswest mirror
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [uswest.ensembl.org:8443] Connection timed out after 10000 milliseconds

Might it be something else? Thanks!

ADD REPLY • link 3.6 years ago tommaso.gastaldi • 0