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
I have a similar problem.
I run the following:
And get the following error:
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".That did not work either.
Would be grateful for any advice!
Best, Robin
Hi, still experiencing the same issue here:
returns
but both the following calls
return the dataframe of names with no issue.
how can i use the getLDS function in the correct way to get the mouse ids together with the human ids ?
thanks!