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getBM error while using bioMart

Hi all,

This script used to work for me and now it doesn't anymore:

ensembl = useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", mirror = "useast")


getBM( attributes = c("ensembl_gene_id", "entrezgene_id", "hgnc_symbol"),
                  filters = "ensembl_gene_id",
                   values = TPM_data$ensembl,
                   mart = ensembl
                  )

This is the error I am getting:

Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"

I tried to solve this by replacing mirrors but it didn't help.

Can anyone please help me to solve this?

Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"

biomart getbm ensembl
• 14,155 views • link
updated by user17394 • user17394 • written by MatStat MatStat

Hi, can you please try just:

ensembl = useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")

Also, which version of R and biomaRt are you using?

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written by Kevin Blighe Kevin Blighe

Hi, Thank you for the prompt reply.

useEnsembl worked for me already. But I did try the line you wrote anyway without the mirror. No error in that line but when I try getBM it doesn't work and gives the same error. 

  ensembl = useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")



TPM_countdata$ensembl <- sapply( strsplit( rownames(TPM_countdata), split="nn+" ), "[", 1 )

#apply gene names on a result table
genemap <- getBM( attributes = c("ensembl_gene_id", "entrezgene_id", "hgnc_symbol"),
                  filters = "ensembl_gene_id",
                  values = TPM_countdata$ensembl,
                  mart = ensembl
                  )

Using: R version 4.0.2 (2020-06-22) bioMart 2.44.1

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written by MatStat MatStat

I see. What is the output of:

str(TPM_countdata$ensembl)

?

Also, from where are you running this command (on a cluster)?

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written by Kevin Blighe Kevin Blighe

Hi Kevin, Well for the first question, it is just a vector containing strings with the names of the genes as "ensembl":

> head(TPM_countdata$ensembl)

[1] "ENSG00000000003" "ENSG00000000419" "ENSG00000000457" "ENSG00000000460" [5] "ENSG00000000938" "ENSG00000000971"

I'm not sure what do you mean in the second question (sorry).

Best

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written by MatStat MatStat

I'm having the exact same issue. Could the servers be down?

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written by koen.vdberge • koen.vdberge

I was also wondering if they are down since I'm using it quite often and had no problems with this script in the past.

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written by MatStat MatStat

Same here. Same error, same script I always use. Changing mirrors doesnt help

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written by dango147 • dango147

I've contacted Ensembl helpdesk now and described the problem. I will update if they'll answer and if the problem is actually central. Unless of course it will be solved here by someone.

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written by MatStat MatStat

Update: I have received the following answer from Ensembl helpdesk:

Hi,

Thanks for reporting the error with the Ensembl website. Apologies for the problems. The issue with Biomart is now fixed.

Best

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written by MatStat MatStat

I have encountered the same error in R version 4.0.2 with biomaRt 2.44.1. Please help!

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written by xiaoyonf • xiaoyonf

It now worked for me. But I have to unload ‘GenomicFeatures’ package, which seems autoload biomaRt that cause version conflict. Thanks!

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written by xiaoyonf • xiaoyonf

We experienced the same http connectivity errors with three Ensembl mirrors yesterday (20200809; useast, uswest and asia). It appears that Ensembl has corrected the error on their end, as bioMart versions <= 2.45.5 still work as expected (e.g. biomaRt_2.42.0 on CentOS 7).

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written by user17394 • user17394

1 answer

My initial assement is that something has changed on the Ensembl website, which now doesn't allow access via http. If you go to http://www.ensembl.org in your browser it will automatically redirect you to use https; the code in biomaRt is failing rather than following the re-direct.

Can you try using the latest development version from GitHub, and let me know if it improves the situation. You can install this via:

BiocManager::install('grimbough/biomaRt')
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written by Mike Smith Mike Smith

I have tried, but still not work. Does the library loading use library(biomaRt)?

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written by xiaoyonf • xiaoyonf

I would suggest starting a new R session. Then you can run:

## This install the latest version of biomaRt
BiocManager::install('grimbough/biomaRt')
## This loads the newly installed package
library(biomaRt)
##  Check the version of the package - the latest is 2.45.5
packageVersion('biomaRt')

If that all looks good, run your biomaRt query and let me know if you still see the error.

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written by Mike Smith Mike Smith

This has worked for me as well. Thank you for the solution.

Hopefully that would work for the rest.

All the best.

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written by MatStat MatStat

Hi, I also encountered the same problem. I tried what you suggested and got:

Error: Failed to install 'biomaRt' from GitHub: (converted from warning) installation of package ‘stringi’ had non-zero exit status

Any suggestions?

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written by HB • HB

Hi,

Try to install the package: 'stringi'. Then, try again and see if it works.

Best

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written by MatStat MatStat

Hi! I tried what you suggest. With the last version of the genome I'd like to investigate it works. But when I try with any less recent release it doesn't work and reports me this error:

Error in bmRequest(request = request, verbose = verbose) : Not Found (HTTP 404).

Can anybody please help me? Thanks!

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written by hopeful-M • hopeful-M

Can you provide an example of the code that leads to the error?

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written by Mike Smith Mike Smith

For example, if I try to use the last version of human genome (v101) it works, but when I try with another one like version 99, it doesn't. Here I paste the code that I use:

library(biomaRt) ensembl = useEnsembl(biomart="ensembl", dataset = "hsapiens_gene_ensembl", version=99)

Thank you so much for your help!

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written by hopeful-M • hopeful-M

This should now be fixed in biomaRt version 2.45.9.

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written by Mike Smith Mike Smith

Hi, I also tiied the lastest version and met the same problems ensembl = useEnsembl(biomart="ensembl", dataset = "hsapiens_gene_ensembl", version=98) Error in bmRequest(request = request, verbose = verbose) : Not Found (HTTP 404). or mart = useMart( host="https://sep2019.archive.ensembl.org", + biomart="ensembl", + dataset="hsapiens_gene_ensembl") Error in bmRequest(request = request, verbose = verbose) : Not Found (HTTP 404). biomart version is 2.45.9 and R version is 4.0.3. Is there any suggestions to solve the problems? thanks so much

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written by wangxujun87 • wangxujun87

Currently, if I go to https://sep2019.archive.ensembl.org/ I get the message:

Server Status 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.

This is a larger Ensembl issue, rather than something we can fix in biomaRt.

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written by Mike Smith Mike Smith

This seems a weird one. If you run the function listEnsemblArchives() do you also get the error? That is the function that tries to read that URL, and in version 2.45.8 it should not be trying to read the http version.

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written by Mike Smith Mike Smith

Just woke up today with the same code working now, so... problem solved I guess

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written by davide.pernici • davide.pernici

Hey,

I installed the package and still have the error

humanmart <- useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", version = "96")
Error in bmRequest(request = request, verbose = verbose) : 
  Not Found (HTTP 404).

humanmart <- useMart(host='apr2019.archive.ensembl.org', dataset="hsapiens_gene_ensembl", biomart='ENSEMBL_MART_ENSEMBL')
Error in bmRequest(request = request, verbose = verbose) : 
  Not Found (HTTP 404).
• 0 views • link
written by mat.lesche • mat.lesche

This code works for me at the moment,but it looks like some of the other archive sites are down (you get a 'down for maintenance' page in a browser) and will produces this same error. Hopefully this is only a temporary thing, but I think it is a server-side Ensembl issue rather than something I can fix in biomaRt or a setting you need.

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written by Mike Smith Mike Smith

This is correct. There are https changes and we're attempting to get this fixed today.

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written by Emily Emily

I'm still having trouble using BiomaRt version 2.45.6 and R version 4.0.3. Is anyone else still running into this issue? Any ideas about workarounds?

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written by kwhiggins27 • kwhiggins27

Same issue with R 4.0.3 and biomaRt 2.45.7. They haven't been able to fix it.

EDIT: Restarted R session and the issue is fixed.

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written by Sandip Darji • Sandip Darji

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