Question: ensembl not working...?
1
gravatar for JoeMG
13 months ago by
JoeMG0
JoeMG0 wrote:

I'm having trouble connecting to the human dataset from ensembl. I've run these scripts hundreds of times and this was the first time I've encountered these errors. Anyone can help?

 

> ensembl <-  useMart("ensembl", dataset="hsapiens_gene_ensembl")
Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
  Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt&redirect=no
> ensembl <-  useMart("ensembl", host="uswest.ensembl.org", dataset="hsapiens_gene_ensembl", ensemblRedirect = FALSE)
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
> ensembl <-  useMart("ensembl", host="useast.ensembl.org", dataset="hsapiens_gene_ensembl", ensemblRedirect = FALSE)
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
> ensembl <-  useMart("ensembl", host="uswest.ensembl.org", dataset="hsapiens_gene_ensembl", ensemblRedirect = FALSE)
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
> ensembl = useMart("ensembl", host="uswest.ensembl.org")
> listDatasets(ensembl)
[1] dataset     description version    
<0 rows> (or 0-length row.names)
> ensembl = useMart("ensembl", host="useast.ensembl.org")
> listDatasets(ensembl)
[1] dataset     description version    
<0 rows> (or 0-length row.names)
> ensembl = useMart("ensembl", host="asia.ensembl.org")
> listDatasets(ensembl)
[1] dataset     description version    
<0 rows> (or 0-length row.names)

 

 

> sessionInfo()

R version 3.4.1 (2017-06-30)

Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] biomaRt_2.32.1                          BiocInstaller_1.26.1                    ggcyto_1.4.1                           
 [4] ggplot2_2.2.1                           flowWorkspace_3.24.4                    ncdfFlow_2.22.2                        
 [7] BH_1.66.0-1                             RcppArmadillo_0.8.400.0.0               flowViz_1.40.0                         
[10] lattice_0.20-35                         flowCore_1.42.3                         BRRR_1.2                               
[13] devtools_1.13.5                         stringr_1.3.0                           VariantAnnotation_1.22.3               
[16] Rsamtools_1.28.0                        SummarizedExperiment_1.6.5              DelayedArray_0.2.7                     
[19] matrixStats_0.53.1                      RMySQL_0.10.14                          DBI_0.8                                
[22] openxlsx_4.0.17                         seqinr_3.4-5                            org.Hs.eg.db_3.4.1                     
[25] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.28.5                  AnnotationDbi_1.38.2                   
[28] Biobase_2.36.2                          BSgenome.Hsapiens.UCSC.hg19_1.4.0       BSgenome_1.44.2                        
[31] rtracklayer_1.36.6                      GenomicRanges_1.28.6                    GenomeInfoDb_1.12.3                    
[34] CRISPRseek_1.16.0                       Biostrings_2.44.2                       XVector_0.16.0                         
[37] IRanges_2.10.5                          S4Vectors_0.14.7                        BiocGenerics_0.22.1                    

loaded via a namespace (and not attached):
 [1] bitops_1.0-6             bit64_0.9-7              progress_1.1.2           httr_1.3.1              
 [5] RColorBrewer_1.1-2       Rgraphviz_2.20.0         tools_3.4.1              R6_2.2.2                
 [9] KernSmooth_2.23-15       lazyeval_0.2.1           colorspace_1.3-2         ade4_1.7-11             
[13] withr_2.1.2              prettyunits_1.0.2        gridExtra_2.3            curl_3.2                
[17] git2r_0.21.0             bit_1.1-12               compiler_3.4.1           graph_1.54.0            
[21] scales_0.5.0             DEoptimR_1.0-8           hexbin_1.27.2            mvtnorm_1.0-7           
[25] robustbase_0.93-0        digest_0.6.15            rrcov_1.4-3              pkgconfig_2.0.1         
[29] rlang_0.2.0              RSQLite_2.1.0            bindr_0.1.1              BiocParallel_1.10.1     
[33] dplyr_0.7.4              RCurl_1.95-4.10          magrittr_1.5             GenomeInfoDbData_0.99.0 
[37] Matrix_1.2-14            Rcpp_0.12.16             munsell_0.4.3            stringi_1.1.7           
[41] yaml_2.1.18              MASS_7.3-49              zlibbioc_1.22.0          plyr_1.8.4              
[45] grid_3.4.1               blob_1.1.1               hash_2.2.6               knitr_1.20              
[49] pillar_1.2.2             corpcor_1.6.9            XML_3.98-1.11            glue_1.2.0              
[53] latticeExtra_0.6-28      data.table_1.10.4-3      gtable_0.2.0             assertthat_0.2.0        
[57] IDPmisc_1.1.17           pcaPP_1.9-73             audio_0.1-5              tibble_1.4.2            
[61] GenomicAlignments_1.12.2 memoise_1.1.0            bindrcpp_0.2.2           cluster_2.0.7-1    

 

biomart ensembl • 366 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by JoeMG0
Answer: ensembl not working...?
0
gravatar for Mike Smith
13 months ago by
Mike Smith3.7k
EMBL Heidelberg / de.NBI
Mike Smith3.7k wrote:

It looks like you haven't posted here before, so I'll just point out that there's a couple of things you can do to increase the likelihood you get a useful answer.  The first is to make sure you tag your post with the name of the package you're trying to use - in this case that's biomaRt - so the package maintainer is alerted.

It's also good to include the output of the function sessionInfo() as this lets people see which version of R and the various packages you're using.  How biomaRt handles redirection to Ensembl mirrors has changed recently, so the advice I give come with the caveat that I'm guessing at the version you're using.

Now for an answer...


The main Ensembl site appears to be down at the moment.  It looks like you've tried to set the host to use a mirror, but you probably also need to set the argument ensemblRedirect = FALSE, otherwise you get redirected to your local mirror anyway.

So the full comand would be:

ensembl = useMart("ensembl", host="useast.ensembl.org", ensemblRedirect = FALSE)
ADD COMMENTlink modified 13 months ago • written 13 months ago by Mike Smith3.7k

Thanks, I get the same with ensemblRedirect = FALSE

The "down" status is probably what I've encountered.

ADD REPLYlink written 13 months ago by JoeMG0

Interesting, for me this works on machine both in Europe and the US:  

library(biomaRt)

ensembl = useMart("ensembl", 
                  host="useast.ensembl.org", 
                  ensemblRedirect = FALSE)

> dim(listDatasets(ensembl))
[1] 98  3
ADD REPLYlink modified 13 months ago • written 13 months ago by Mike Smith3.7k

Maybe a local issue (middle east). The bit bucket doesn't pour my way...

> ensembl = useMart("ensembl", host="useast.ensembl.org", ensemblRedirect = FALSE)
> ensembl
Object of class 'Mart':
 Using the ENSEMBL_MART_ENSEMBL BioMart database
 Using the  dataset
> dim(listDatasets(ensembl))
[1] 0 3

ADD REPLYlink written 13 months ago by JoeMG0
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