BiomaRt connection error: Could not connect to mysql database ensembl_mart_104
1
1
Entering edit mode
Anand ▴ 10
@Anand-24608
Last seen 7 days ago
Australia

Hi everyone.

Up until this afternoon, never had a problem with biomaRT and the following code:

myMart <- useMart(biomart="ENSEMBL_MART_ENSEMBL")
mouse.anno <- useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl")

gene <- getBM(attributes=c("gene_biotype", "external_gene_name", "description"), filters = "external_gene_name", values=res.df$external_gene_name, mart=mouse.anno)

But now, i'm getting this eror:

Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery, : Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_104: DBI connect('database=ensembl_mart_104;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_104/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.

Is this is a congestion issue? Is there alternative code?

Thanks.

```r sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale: [1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8

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

other attached packages: [1] viridis_0.6.1 viridisLite_0.4.0 hrbrthemes_0.8.0 enrichR_3.0
[5] ggvenn_0.1.8 scales_1.1.1 pheatmap_1.0.12 enrichplot_1.10.2
[9] msigdbr_7.4.1 clusterProfiler_3.18.1 gprofiler2_0.2.0 GSVA_1.38.2
[13] GSEABase_1.52.1 graph_1.68.0 annotate_1.68.0 XML_3.99-0.6
[17] VennDiagram_1.6.20 futile.logger_1.4.3 ggrepel_0.9.1 patchwork_1.1.1
[21] IsoformSwitchAnalyzeR_1.12.0 DEXSeq_1.36.0 DESeq2_1.30.1 ggpubr_0.4.0
[25] RColorBrewer_1.1-2 org.Mm.eg.db_3.12.0 gplots_3.1.1 Glimma_2.0.0
[29] tximport_1.18.0 DT_0.18 plotly_4.9.3 EnsDb.Mmusculus.v79_2.99.0
[33] ensembldb_2.14.1 AnnotationFilter_1.14.0 GenomicFeatures_1.42.3 AnnotationDbi_1.52.0
[37] gt_0.3.0 cowplot_1.1.1 RUVSeq_1.24.0 forcats_0.5.1
[41] stringr_1.4.0 dplyr_1.0.6 purrr_0.3.4 readr_1.4.0
[45] tidyr_1.1.3 tibble_3.1.2 ggplot2_3.3.3 tidyverse_1.3.1
[49] EDASeq_2.24.0 ShortRead_1.48.0 GenomicAlignments_1.26.0 SummarizedExperiment_1.20.0 [53] MatrixGenerics_1.2.1 matrixStats_0.59.0 Rsamtools_2.6.0 GenomicRanges_1.42.0
[57] GenomeInfoDb_1.26.7 Biostrings_2.58.0 XVector_0.30.0 IRanges_2.24.1
[61] S4Vectors_0.28.1 BiocParallel_1.24.1 Biobase_2.50.0 BiocGenerics_0.36.1
[65] biomaRt_2.46.3 edgeR_3.32.1 limma_3.46.0

loaded via a namespace (and not attached): [1] rappdirs_0.3.3 rtracklayer_1.50.0 R.methodsS3_1.8.1 knitr_1.33
[5] bit64_4.0.5 aroma.light_3.20.0 DelayedArray_0.16.3 R.utils_2.10.1
[9] data.table_1.14.0 hwriter_1.3.2 RCurl_1.98-1.3 generics_0.1.0
[13] lambda.r_1.2.4 RSQLite_2.2.7 shadowtext_0.0.8 bit_4.0.4
[17] xml2_1.3.2 lubridate_1.7.10 httpuv_1.6.1 assertthat_0.2.1
[21] xfun_0.23 hms_1.1.0 evaluate_0.14 babelgene_21.4
[25] promises_1.2.0.1 fansi_0.5.0 progress_1.2.2 caTools_1.18.2
[29] dbplyr_2.1.1 readxl_1.3.1 igraph_1.2.6 DBI_1.1.1
[33] geneplotter_1.68.0 htmlwidgets_1.5.3 ellipsis_0.3.2 backports_1.2.1
[37] vctrs_0.3.8 abind_1.4-5 cachem_1.0.5 withr_2.4.2
[41] ggforce_0.3.3 BSgenome_1.58.0 prettyunits_1.1.1 DOSE_3.16.0
[45] lazyeval_0.2.2 crayon_1.4.1 genefilter_1.72.1 labeling_0.4.2
[49] pkgconfig_2.0.3 tweenr_1.0.2 ProtGenerics_1.22.0 rlang_0.4.11
[53] lifecycle_1.0.0 downloader_0.4 extrafontdb_1.0 BiocFileCache_1.14.0
[57] modelr_0.1.8 AnnotationHub_2.22.1 cellranger_1.1.0 polyclip_1.10-0
[61] Matrix_1.3-4 carData_3.0-4 tximeta_1.8.5 reprex_2.0.0
[65] rjson_0.2.20 png_0.1-7 bitops_1.0-7 R.oo_1.24.0
[69] KernSmooth_2.23-20 blob_1.2.1 qvalue_2.22.0 jpeg_0.1-8.1
[73] rstatix_0.7.0 ggsignif_0.6.1 memoise_2.0.0 magrittr_2.0.1
[77] plyr_1.8.6 zlibbioc_1.36.0 scatterpie_0.1.6 compiler_4.0.5
[81] cli_2.5.0 formatR_1.11 MASS_7.3-54 tidyselect_1.1.1
[85] stringi_1.6.2 yaml_2.2.1 GOSemSim_2.16.1 askpass_1.1
[89] locfit_1.5-9.4 latticeExtra_0.6-29 fastmatch_1.1-0 tools_4.0.5
[93] rio_0.5.26 rstudioapi_0.13 foreign_0.8-81 gridExtra_2.3
[97] farver_2.1.0 ggraph_2.0.5 rvcheck_0.1.8 digest_0.6.27
[101] BiocManager_1.30.15 shiny_1.6.0 Rcpp_1.0.6 car_3.0-10
[105] broom_0.7.6 BiocVersion_3.12.0 later_1.2.0 gdtools_0.2.3
[109] httr_1.4.2 colorspace_2.0-1 rvest_1.0.0 fs_1.5.0
[113] splines_4.0.5 statmod_1.4.36 graphlayouts_0.7.1 systemfonts_1.0.2
[117] xtable_1.8-4 jsonlite_1.7.2 futile.options_1.0.1 tidygraph_1.2.0
[121] R6_2.5.0 pillar_1.6.1 htmltools_0.5.1.1 mime_0.10
[125] DRIMSeq_1.18.0 glue_1.4.2 fastmap_1.1.0 interactiveDisplayBase_1.28.0 [129] fgsea_1.16.0 utf8_1.2.1 lattice_0.20-44 curl_4.3.1
[133] gtools_3.8.2 Rttf2pt1_1.3.8 zip_2.2.0 GO.db_3.12.1
[137] openxlsx_4.2.3 openssl_1.4.4 survival_3.2-11 rmarkdown_2.8
[141] munsell_0.5.0 DO.db_2.9 GenomeInfoDbData_1.2.4 haven_2.4.1
[145] reshape2_1.4.4 gtable_0.3.0 extrafont_0.17

biomaRt connection sql • 853 views
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0
Entering edit mode

Hi, I have the same trouble since yesterday and I use ensembl archive : ```r

mart=useMart(biomart="ensembl",dataset = "sscrofa_gene_ensembl",host = "aug2020.archive.ensembl.org")

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0
Entering edit mode

Same error here for mouse queries, until I restart R session and got a new error Error in do.call(c, obj@httr_config) : no slot of name "httr_config" for this object of class "Mart" Seems a problem with the ensembl server but not sure! Any suggestions Mike Smith? Thanks

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Entering edit mode

Joan Miró This is a different error, an possibly indicates that you're using a saved object from an older version of biomaRt. Please open a new thread with the details of the query you're running, sessionInfo() etc.

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3
Entering edit mode
Mike Smith ★ 5.0k
@mike-smith
Last seen 1 day ago
EMBL Heidelberg / de.NBI

The error you've encountered ("Query ERROR: caught BioMart::Exception::Database") comes from the Ensembl BioMart server. If that has a problem, there's nothing biomaRt can really do to help. The source of the data is broken, and you have to wait for Ensembl to fix it. However, for me the code now works so hopefully it is now resolved:

library(biomaRt)

mouse.anno <- useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl")

getBM(attributes=c("gene_biotype", "external_gene_name", "description"), 
      filters = "external_gene_name", 
      values = "Cdc6", 
      mart = mouse.anno)
#>     gene_biotype external_gene_name
#> 1 protein_coding               Cdc6
#>                                                 description
#> 1 cell division cycle 6 [Source:MGI Symbol;Acc:MGI:1345150]

If you encounter this again, one option is to try querying one of the Ensembl mirrors, which may be working even if the main site has a problem. You can do that by creating you Mart object with the function useEnsembl() rather than useMart()

mouse.anno <- useEnsembl(biomart = "genes", 
                         dataset = "mmusculus_gene_ensembl", 
                         mirror = "asia")

Values for the mirror argument are: www, useast, uswest, asia.

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0
Entering edit mode

Thanks Mike Smith, yes now it works! Thank you for the suggestions!

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