biomaRt server error, and mirrors do not help
2
2
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kieran.short ▴ 40
@693804cb
Last seen 2.1 years ago
Australia

Hi, I'm trying to convert/remap about 20k mouse gene names to human gene names using biomaRt and it isn't working. I get server errors when the lookup is performed. I've seen multiple posts on errors with biomaRt. None of the fixes mentioned in there (e.g. use mirrors, check the availability of the different marts -- which are available) seem to work. Something is going on with the server and mirrors.

I have some example code with a single gene name in it for testing.

If using the normal Ensembl server for biomaRt:

library(biomaRt)

mouse = useMart("ensembl",
                  dataset="mmusculus_gene_ensembl")

human = useMart("ensembl",
                dataset="hsapiens_gene_ensembl")

getLDS("mgi_symbol","mgi_symbol", "Rpl18", mouse, "hgnc_symbol", martL = human)
Error: biomaRt has encountered an unexpected server error.
Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)

Okay, so I then tried a mirror:

library(biomaRt)

mouse = useMart(biomart="ENSEMBL_MART_ENSEMBL",
                  dataset="mmusculus_gene_ensembl", 
                  host="uswest.ensembl.org")

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

getLDS("mgi_symbol","mgi_symbol", "Rpl18", mouse, "hgnc_symbol", martL = human)
Error: biomaRt has encountered an unknown server error. HTTP error code: 502
Please report this on the Bioconductor support site at https://support.bioconductor.org/
Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)

So I tried the "useast" and "asia" mirrors, which also failed the same way as the "uswest" mirror.

If I check the available marts, they are present:

> listMarts()
               biomart                version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 106
2   ENSEMBL_MART_MOUSE      Mouse strains 106
3     ENSEMBL_MART_SNP  Ensembl Variation 106
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 106

My session info is:

sessionInfo( )

R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8   
 [6] LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           LC_TELEPHONE=C        
[11] LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

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

other attached packages:
[1] biomaRt_2.51.4

loaded via a namespace (and not attached):
 [1] KEGGREST_1.34.0        progress_1.2.2         tidyselect_1.1.2       xfun_0.30              purrr_0.3.4           
 [6] vctrs_0.4.1            generics_0.1.2         stats4_4.1.3           BiocFileCache_2.2.1    utf8_1.2.2            
[11] blob_1.2.3             XML_3.99-0.9           rlang_1.0.2            pillar_1.7.0           glue_1.6.2            
[16] DBI_1.1.2              rappdirs_0.3.3         BiocGenerics_0.40.0    bit64_4.0.5            dbplyr_2.1.1          
[21] GenomeInfoDbData_1.2.7 lifecycle_1.0.1        stringr_1.4.0          zlibbioc_1.40.0        Biostrings_2.62.0     
[26] memoise_2.0.1          Biobase_2.54.0         knitr_1.39             IRanges_2.28.0         fastmap_1.1.0         
[31] GenomeInfoDb_1.30.1    curl_4.3.2             AnnotationDbi_1.56.2   fansi_1.0.3            Rcpp_1.0.8.3          
[36] filelock_1.0.2         cachem_1.0.6           S4Vectors_0.32.4       XVector_0.34.0         bit_4.0.4             
[41] hms_1.1.1              png_0.1-7              digest_0.6.29          stringi_1.7.6          dplyr_1.0.8           
[46] cli_3.3.0              tools_4.1.3            bitops_1.0-7           magrittr_2.0.3         RCurl_1.98-1.6        
[51] RSQLite_2.2.12         tibble_3.1.6           crayon_1.5.1           pkgconfig_2.0.3        ellipsis_0.3.2        
[56] xml2_1.3.3             prettyunits_1.1.1      assertthat_0.2.1       httr_1.4.2             rstudioapi_0.13       
[61] R6_2.5.1               compiler_4.1.3

To verify what is happening, I tried replicating it on another server. I found that not using a mirror on the second server gave the same result as the first server, i.e.

Error: biomaRt has encountered an unexpected server error.
Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)

Using the mirrors on the second server gave a different error:

library(biomaRt)

mouse = useMart(biomart="ENSEMBL_MART_ENSEMBL",
                 dataset="mmusculus_gene_ensembl", 
                 host="asia.ensembl.org")

human = useMart(biomart="ENSEMBL_MART_ENSEMBL",
                 dataset="hsapiens_gene_ensembl", 
                 host="asia.ensembl.org")
getLDS("mgi_symbol","mgi_symbol", "Rpl18", mouse, "hgnc_symbol", martL = human)
Error in .createErrorMessage(error_code = status_code(res), host = host) : 
  object 'err_msg' not found

Session info on the second server:

R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] biomaRt_2.46.3

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3         pillar_1.7.0         compiler_4.0.5      
 [4] dbplyr_2.1.1         prettyunits_1.1.1    tools_4.0.5         
 [7] progress_1.2.2       digest_0.6.29        bit_4.0.4           
[10] tibble_3.1.6         RSQLite_2.2.10       memoise_1.1.0       
[13] BiocFileCache_1.14.0 lifecycle_1.0.1      pkgconfig_2.0.3     
[16] rlang_1.0.2          DBI_1.1.0            cli_3.2.0           
[19] curl_4.3             parallel_4.0.5       stringr_1.4.0       
[22] httr_1.4.2           dplyr_1.0.8          xml2_1.3.2          
[25] rappdirs_0.3.3       generics_0.1.2       S4Vectors_0.28.1    
[28] vctrs_0.3.8          askpass_1.1          IRanges_2.24.1      
[31] hms_1.1.1            tidyselect_1.1.2     stats4_4.0.5        
[34] bit64_4.0.5          glue_1.6.2           Biobase_2.50.0      
[37] R6_2.5.1             fansi_1.0.2          AnnotationDbi_1.52.0
[40] XML_3.99-0.9         purrr_0.3.4          blob_1.2.2          
[43] magrittr_2.0.2       ellipsis_0.3.2       BiocGenerics_0.36.0 
[46] assertthat_0.2.1     utf8_1.2.2           stringi_1.5.3       
[49] openssl_1.4.3        crayon_1.5.0

My two servers aren't running the same version of biomaRt, R, or OS. That might explain the discrepancy in the mirror errors between those two tests. Regardless, it isn't working.

Can anyone please help?

thanks, K

ensembl biomaRt R • 7.3k views
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2
Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 12 hours ago
EMBL Heidelberg

There seems to be an issue with the linked dataset queries after the latest update to Ensembl version 106. I've reported this to the Ensembl help desk, hopefully there will be a fix soon. As a temporary workaround you can try using the version 105 archive.

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Thanks Mike. For anyone on here trying to work around this issue: try setting host to "dec2021.archive.ensembl.org". For example out of my initial post: " human = useMart(biomart="ensembl", dataset = "hsapiens_gene_ensembl", verbose = TRUE, host = "dec2021.archive.ensembl.org") "

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1
Entering edit mode

Dear Mike,

I have been using the dec2021.archive.ensembl.org and was working well. over the last couple of days, I have been getting the following error

Loading required package: biomaRt Ensembl site unresponsive, trying www mirror Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [dec2021.archive.ensembl.org:443] Connection timed out after 10001 milliseconds

Would you please help? Thank you

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0
Entering edit mode

Hi kieran, i met the same problem, and "dec2021.archive.ensembl.org" was working well for me, thank you!

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@james-w-macdonald-5106
Last seen 15 hours ago
United States

biomart getLDS giving errors.

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