502 error biomaRt getLDS()
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1
Entering edit mode
Pez ▴ 10
@724e8e11
Last seen 13 days ago
Australia

I have been trying to convert ensembl gene IDs between species, but I keep getting a 502 error that tells me to report it here.

library(biomaRt)
hsa_mart<- useEnsembl(biomart="genes",dataset="hsapiens_gene_ensembl", mirror="useast")
aca_mart<- useEnsembl("ensembl",dataset="acarolinensis_gene_ensembl", mirror="useast")

aca_hsa_mart<- getLDS(attributes=c("entrezgene_accession","entrezgene_id","uniprot_gn_id", "ensembl_gene_id"),
                      mart=hsa_mart,values="ENSG00000049130", filters="ensembl_gene_id",
                      attributesL=c("entrezgene_accession","entrezgene_id","uniprot_gn_id", "ensembl_gene_id"),
                      martL=aca_mart,
                      verbose=TRUE)

I get the error at the getLDS() step.

"<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' formatter = 'TSV' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'entrezgene_accession'/><Attribute name = 'entrezgene_id'/><Attribute name = 'uniprot_gn_id'/><Attribute name = 'ensembl_gene_id'/><Filter name = "ensembl_gene_id" value = "ENSG00000049130" /></Dataset><Dataset name = 'acarolinensis_gene_ensembl' ><Attribute name = 'entrezgene_accession'/><Attribute name = 'entrezgene_id'/><Attribute name = 'uniprot_gn_id'/><Attribute name = 'ensembl_gene_id'/></Dataset></Query> 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)"

I also tried using the "www" mirror and I get the same answer. I also tried on a different internet connection with the same error. Also I can use the command getBM() without issue.

Any ideas?


sessionInfo( )


"R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_Australia.utf8 
[2] LC_CTYPE=English_Australia.utf8   
[3] LC_MONETARY=English_Australia.utf8
[4] LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.utf8    

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] biomaRt_2.58.2

loaded via a namespace (and not attached):
 [1] rappdirs_0.3.3          utf8_1.2.4             
 [3] generics_0.1.3          xml2_1.3.6             
 [5] bitops_1.0-7            RSQLite_2.3.5          
 [7] stringi_1.8.3           hms_1.1.3              
 [9] digest_0.6.34           magrittr_2.0.3         
[11] evaluate_0.23           pkgload_1.3.4          
[13] fastmap_1.1.1           blob_1.2.4             
[15] progress_1.2.3          AnnotationDbi_1.64.1   
[17] GenomeInfoDb_1.38.5     DBI_1.2.1              
[19] httr_1.4.7              purrr_1.0.2            
[21] fansi_1.0.6             XML_3.99-0.16.1        
[23] Biostrings_2.70.2       cli_3.6.2              
[25] rlang_1.1.3             crayon_1.5.2           
[27] dbplyr_2.4.0            XVector_0.42.0         
[29] Biobase_2.62.0          bit64_4.0.5            
[31] withr_3.0.0             cachem_1.0.8           
[33] yaml_2.3.8              tools_4.3.2            
[35] memoise_2.0.1           dplyr_1.1.4            
[37] filelock_1.0.3          GenomeInfoDbData_1.2.11
[39] BiocGenerics_0.48.1     curl_5.2.0             
[41] vctrs_0.6.5             R6_2.5.1               
[43] png_0.1-8               stats4_4.3.2           
[45] lifecycle_1.0.4         BiocFileCache_2.10.1   
[47] zlibbioc_1.48.0         KEGGREST_1.42.0        
[49] stringr_1.5.1           S4Vectors_0.40.2       
[51] IRanges_2.36.0          bit_4.0.5              
[53] pkgconfig_2.0.3         pillar_1.9.0           
[55] glue_1.7.0              tidyselect_1.2.0       
[57] xfun_0.41               tibble_3.2.1           
[59] rstudioapi_0.15.0       knitr_1.45             
[61] htmltools_0.5.7         rmarkdown_2.25         
[63] compiler_4.3.2          prettyunits_1.2.0      
[65] RCurl_1.98-1.14
ensembldb biomaRt • 155 views
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0
Entering edit mode

I have a similar problem.

I run the following:

ensembl <- useEnsembl("genes")
ensembl_Mmus <- useDataset("mmusculus_gene_ensembl",mart = ensembl)
ensembl_Pmur <- useDataset("pmuralis_gene_ensembl",mart = ensembl)
annot_table <- getLDS(mart = ensembl_Pmur, 
                      attributes = c('external_gene_name'),
                      martL = ensembl_Mmus, 
                      attributesL = c('external_gene_name'))

And get the following error:

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

I tried all the mirrors using eg mirror = "www", none work. When I use "useast" I get the same error code as the author above (502). When I use "asia" I instead get error code 404.

I also tried using the four first archives (without setting mirrors) using e.g. host = "https://oct2022.archive.ensembl.org".

head(listEnsemblArchives())
            name     date                                 url version current_release
1 Ensembl GRCh37 Feb 2014          https://grch37.ensembl.org  GRCh37                
2    Ensembl 111 Jan 2024 https://jan2024.archive.ensembl.org     111               *
3    Ensembl 110 Jul 2023 https://jul2023.archive.ensembl.org     110                
4    Ensembl 109 Feb 2023 https://feb2023.archive.ensembl.org     109                
5    Ensembl 108 Oct 2022 https://oct2022.archive.ensembl.org     108                
6    Ensembl 107 Jul 2022 https://jul2022.archive.ensembl.org     107                

That did not work either.

Would be grateful for any advice!

Best, Robin

> sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_Sweden.utf8  LC_CTYPE=English_Sweden.utf8    LC_MONETARY=English_Sweden.utf8
[4] LC_NUMERIC=C                    LC_TIME=English_Sweden.utf8    

time zone: Europe/Stockholm
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] biomaRt_2.58.2              scmap_1.24.0                SingleCellExperiment_1.24.0
 [4] SummarizedExperiment_1.32.0 Biobase_2.62.0              GenomicRanges_1.54.1       
 [7] GenomeInfoDb_1.38.5         IRanges_2.36.0              S4Vectors_0.40.2           
[10] BiocGenerics_0.48.1         MatrixGenerics_1.14.0       matrixStats_1.0.0          
[13] lubridate_1.9.3             forcats_1.0.0               stringr_1.5.1              
[16] dplyr_1.1.3                 purrr_1.0.2                 readr_2.1.5                
[19] tidyr_1.3.0                 tibble_3.2.1                ggplot2_3.4.4              
[22] tidyverse_2.0.0            

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.21        splines_4.3.2           later_1.3.1            
  [4] filelock_1.0.3          bitops_1.0-7            polyclip_1.10-4        
  [7] XML_3.99-0.16.1         fastDummies_1.7.3       lifecycle_1.0.4        
 [10] globals_0.16.2          lattice_0.22-5          MASS_7.3-60            
 [13] magrittr_2.0.3          plotly_4.10.4           rmarkdown_2.25         
 [16] yaml_2.3.7              httpuv_1.6.11           Seurat_5.0.1           
 [19] sctransform_0.4.1       spam_2.10-0             sp_2.0-0               
 [22] spatstat.sparse_3.0-2   reticulate_1.32.0       cowplot_1.1.3          
 [25] pbapply_1.7-2           DBI_1.2.1               RColorBrewer_1.1-3     
 [28] pkgload_1.3.4           abind_1.4-5             zlibbioc_1.48.0        
 [31] Rtsne_0.16              RCurl_1.98-1.14         rappdirs_0.3.3         
 [34] GenomeInfoDbData_1.2.11 ggrepel_0.9.3           irlba_2.3.5.1          
 [37] listenv_0.9.1           spatstat.utils_3.0-3    goftest_1.2-3          
 [40] RSpectra_0.16-1         spatstat.random_3.1-6   fitdistrplus_1.1-11    
 [43] parallelly_1.36.0       leiden_0.4.3.1          codetools_0.2-19       
 [46] DelayedArray_0.28.0     xml2_1.3.6              tidyselect_1.2.0       
 [49] farver_2.1.1            BiocFileCache_2.10.1    spatstat.explore_3.2-3 
 [52] jsonlite_1.8.4          e1071_1.7-14            ellipsis_0.3.2         
 [55] progressr_0.14.0        ggridges_0.5.6          survival_3.5-7         
 [58] progress_1.2.3          tools_4.3.2             ica_1.0-3              
 [61] Rcpp_1.0.11             glue_1.6.2              gridExtra_2.3          
 [64] SparseArray_1.2.3       xfun_0.39               withr_3.0.0            
 [67] fastmap_1.1.1           fansi_1.0.4             digest_0.6.31          
 [70] timechange_0.3.0        R6_2.5.1                mime_0.12              
 [73] colorspace_2.1-0        scattermore_1.2         tensor_1.5             
 [76] spatstat.data_3.0-4     RSQLite_2.3.5           utf8_1.2.3             
 [79] generics_0.1.3          data.table_1.14.8       class_7.3-22           
 [82] prettyunits_1.2.0       httr_1.4.7              htmlwidgets_1.6.4      
 [85] S4Arrays_1.2.0          uwot_0.1.16             pkgconfig_2.0.3        
 [88] gtable_0.3.4            blob_1.2.4              lmtest_0.9-40          
 [91] XVector_0.42.0          htmltools_0.5.7         dotCall64_1.1-1        
 [94] SeuratObject_5.0.1      scales_1.3.0            png_0.1-8              
 [97] knitr_1.45              rstudioapi_0.15.0       tzdb_0.4.0             
[100] reshape2_1.4.4          curl_5.2.0              nlme_3.1-164           
[103] cachem_1.0.8            proxy_0.4-27            zoo_1.8-12             
[106] KernSmooth_2.23-22      parallel_4.3.2          miniUI_0.1.1.1         
[109] AnnotationDbi_1.64.1    pillar_1.9.0            grid_4.3.2             
[112] vctrs_0.6.3             RANN_2.6.1              promises_1.2.1         
[115] randomForest_4.7-1.1    dbplyr_2.4.0            xtable_1.8-4           
[118] cluster_2.1.6           evaluate_0.23           cli_3.6.1              
[121] compiler_4.3.2          rlang_1.1.1             crayon_1.5.2           
[124] future.apply_1.11.1     labeling_0.4.3          plyr_1.8.8             
[127] stringi_1.7.12          viridisLite_0.4.2       googleVis_0.7.1        
[130] deldir_1.0-9            Biostrings_2.70.2       munsell_0.5.0          
[133] lazyeval_0.2.2          spatstat.geom_3.2-5     Matrix_1.6-4           
[136] RcppHNSW_0.5.0          hms_1.1.3               patchwork_1.2.0        
[139] bit64_4.0.5             future_1.33.1           KEGGREST_1.42.0        
[142] shiny_1.8.0             ROCR_1.0-11             igraph_1.5.1           
[145] memoise_2.0.1           bit_4.0.5
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