biomaRt getLDS server error
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Entering edit mode
@floriandeckert-13733
Last seen 7 weeks ago
Austria

Hello forum,

Over the past weeks my scripts using biomaRt fail. I figured out that something is wrong with the getLDS function which triggeres an Error (Error: biomaRt has encountered an unexpected server error.). Its reproducable with the code sniped from the tutorial. The Mart objects get created but getLDS fails which is odd.


human <- useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl")
mouse <- useEnsembl("ensembl", dataset = "mmusculus_gene_ensembl")

getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"),
       filters = "hgnc_symbol", values = "TP53",
       mart = human,
       attributesL = c("refseq_mrna","chromosome_name","start_position"), 
       martL = mouse)

When I set the mirror manually I get another error message from getLDS (Error in .createErrorMessage(error_code = status_code(res), host = host): object 'err_msg' not found)


human <- useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl", mirror="asia")
mouse <- useEnsembl("ensembl", dataset = "mmusculus_gene_ensembl", mirror="asia")

getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"),
       filters = "hgnc_symbol", values = "TP53",
       mart = human,
       attributesL = c("refseq_mrna","chromosome_name","start_position"), 
       martL = mouse)

Can anyone reproduce the error and help me with a workaround?

Best, Florian


R version 4.1.0 (2021-05-18)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.2 (Ootpa)

Matrix products: default
BLAS/LAPACK: /home/fdeckert/bin/miniconda3/envs/r.4.1.0-FD20200109SPLENO/lib/libopenblasp-r0.3.15.so

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

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

other attached packages:
[1] biomaRt_2.50.3

loaded via a namespace (and not attached):
 [1] KEGGREST_1.34.0        pbdZMQ_0.3-7           progress_1.2.2        
 [4] tidyselect_1.1.2       repr_1.1.4             purrr_0.3.4           
 [7] generics_0.1.2         vctrs_0.4.1            htmltools_0.5.2       
[10] stats4_4.1.0           BiocFileCache_2.2.1    base64enc_0.1-3       
[13] utf8_1.2.2             blob_1.2.3             XML_3.99-0.9          
[16] rlang_1.0.2            pillar_1.7.0           withr_2.5.0           
[19] glue_1.6.2             DBI_1.1.2              rappdirs_0.3.3        
[22] BiocGenerics_0.40.0    bit64_4.0.5            dbplyr_2.1.1          
[25] uuid_1.1-0             GenomeInfoDbData_1.2.7 lifecycle_1.0.1       
[28] stringr_1.4.0          zlibbioc_1.40.0        Biostrings_2.62.0     
[31] memoise_2.0.1          evaluate_0.15          Biobase_2.54.0        
[34] IRanges_2.28.0         fastmap_1.1.0          GenomeInfoDb_1.30.1   
[37] curl_4.3.2             AnnotationDbi_1.56.2   fansi_1.0.3           
[40] IRdisplay_1.1          Rcpp_1.0.8.3           filelock_1.0.2        
[43] cachem_1.0.6           IRkernel_1.3           S4Vectors_0.32.4      
[46] jsonlite_1.8.0         XVector_0.34.0         bit_4.0.4             
[49] hms_1.1.1              png_0.1-7              digest_0.6.29         
[52] stringi_1.7.6          dplyr_1.0.9            cli_3.3.0             
[55] tools_4.1.0            bitops_1.0-7           magrittr_2.0.3        
[58] tibble_3.1.7           RCurl_1.98-1.6         RSQLite_2.2.13        
[61] crayon_1.5.1           pkgconfig_2.0.3        ellipsis_0.3.2        
[64] xml2_1.3.3             prettyunits_1.1.1      assertthat_0.2.1      
[67] httr_1.4.3             R6_2.5.1               compiler_4.1.0
biomaRt Bioma • 138 views
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Entering edit mode

I am sorry for crossposting, the problem was posted here and here already. A fix to the problem is to use a archive verison:

human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "https://dec2021.archive.ensembl.org/") 
mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = "https://dec2021.archive.ensembl.org/")

Best, Florian

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