getBM error while using bioMart
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Entering edit mode
2.5 years ago
MatStat ▴ 160

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$ensembl, mart = ensembl )  This is the error I am getting: Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no" I tried to solve this by replacing mirrors but it didn't help. Can anyone please help me to solve this? Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no" biomart getBM ensembl • 5.5k views ADD COMMENT 2 Entering edit mode I'm having the exact same issue. Could the servers be down? ADD REPLY 2 Entering edit mode I was also wondering if they are down since I'm using it quite often and had no problems with this script in the past. ADD REPLY 1 Entering edit mode Same here. Same error, same script I always use. Changing mirrors doesnt help ADD REPLY 2 Entering edit mode I've contacted Ensembl helpdesk now and described the problem. I will update if they'll answer and if the problem is actually central. Unless of course it will be solved here by someone. ADD REPLY 1 Entering edit mode Update: I have received the following answer from Ensembl helpdesk: Hi, Thanks for reporting the error with the Ensembl website. Apologies for the problems. The issue with Biomart is now fixed. Best ADD REPLY 2 Entering edit mode I have encountered the same error in R version 4.0.2 with biomaRt 2.44.1. Please help! ADD REPLY 1 Entering edit mode Hi, can you please try just: ensembl = useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")  Also, which version of R and biomaRt are you using? ADD REPLY 1 Entering edit mode Hi, Thank you for the prompt reply. useEnsembl worked for me already. But I did try the line you wrote anyway without the mirror. No error in that line but when I try getBM it doesn't work and gives the same error.  ensembl = useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") TPM_countdata$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$ensembl, mart = ensembl )  Using: R version 4.0.2 (2020-06-22) bioMart 2.44.1 ADD REPLY 0 Entering edit mode I see. What is the output of: str(TPM_countdata$ensembl)


?

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

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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 ADD REPLY 1 Entering edit mode It now worked for me. But I have to unload ‘GenomicFeatures’ package, which seems autoload biomaRt that cause version conflict. Thanks! ADD REPLY 0 Entering edit mode 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). ADD REPLY 5 Entering edit mode 2.5 years ago Mike Smith ★ 2.0k 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')  ADD COMMENT 1 Entering edit mode This is correct. There are https changes and we're attempting to get this fixed today. ADD REPLY 1 Entering edit mode 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? ADD REPLY 0 Entering edit mode 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. ADD REPLY 0 Entering edit mode I have tried, but still not work. Does the library loading use library(biomaRt)? ADD REPLY 3 Entering edit mode 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. ADD REPLY 0 Entering edit mode Worked for me! Thanks ADD REPLY 0 Entering edit mode This has worked for me as well. Thank you for the solution. Hopefully that would work for the rest. All the best. ADD REPLY 0 Entering edit mode 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? ADD REPLY 1 Entering edit mode Hi, Try to install the package: 'stringi'. Then, try again and see if it works. Best ADD REPLY 0 Entering edit mode 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! ADD REPLY 0 Entering edit mode Can you provide an example of the code that leads to the error? ADD REPLY 0 Entering edit mode 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! ADD REPLY 0 Entering edit mode This should now be fixed in biomaRt version 2.45.9. ADD REPLY 0 Entering edit mode 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 ADD REPLY 0 Entering edit mode 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. ADD REPLY 0 Entering edit mode I still have the same damn error even after this (biomaRt version changed), can anyone help me? packageVersion('biomaRt') [1] ‘2.45.8’ getBM(filters="ensembl_gene_id", attributes=c("ensembl_gene_id", "external_gene_name"), values = tmp$genes, mart = ensembl)

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

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

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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) :

humanmart <- useMart(host='apr2019.archive.ensembl.org', dataset="hsapiens_gene_ensembl", biomart='ENSEMBL_MART_ENSEMBL')
Error in bmRequest(request = request, verbose = verbose) :

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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.