Question

Error: 1: Extra content at the end of the document in using biomaRt

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rubi ▴ 110

@rubi-6462

Last seen 6.4 years ago

Hi,

I'm trying to get mouse Entrez IDs of Ensembl IDs and thought that using biomaRt will be the right thing to do.

So I installed biomaRt and trying to run:

> mart <- useMart(biomart="ensembl", dataset="mmusculus_gene_ensembl")

or

> listEnsembl()

I'm getting this error:

Extra content at the end of the document
Error: 1: Extra content at the end of the document

Help would be appreciated

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] RCurl_1.95-4.8                         bitops_1.0-6                          
 [3] biomaRt_2.28.0                         BiocInstaller_1.22.3                  
 [5] PCGSE_0.2                              MASS_7.3-45                           
 [7] RMTstat_0.3                            safe_3.12.0                           
 [9] SparseM_1.7                            data.table_1.9.6                      
[11] asbio_1.3-4                            gridExtra_2.2.1                       
[13] org.Mm.eg.db_3.3.0                     TxDb.Mmusculus.UCSC.mm10.ensGene_3.2.2
[15] GenomicFeatures_1.24.5                 AnnotationDbi_1.34.4                  
[17] GenomicRanges_1.24.2                   GenomeInfoDb_1.8.3                    
[19] IRanges_2.6.1                          S4Vectors_0.10.3                      
[21] gageData_2.10.0                        gage_2.22.0                           
[23] cellrangerRkit_0.99.0                  Rmisc_1.5                             
[25] plyr_1.8.4                             lattice_0.20-33                       
[27] bit64_0.9-5                            bit_1.1-12                            
[29] ggplot2_2.1.0                          RColorBrewer_1.1-2                    
[31] Biobase_2.32.0                         BiocGenerics_0.18.0                   
[33] Matrix_1.2-6                          

loaded via a namespace (and not attached):
 [1] deSolve_1.13               KEGGREST_1.12.2            SummarizedExperiment_1.2.3 rhdf5_2.16.0              
 [5] colorspace_1.2-6           rtracklayer_1.32.2         chron_2.3-47               XML_3.98-1.4              
 [9] DBI_0.5                    BiocParallel_1.6.6         multcompView_0.1-7         zlibbioc_1.18.0           
[13] Biostrings_2.40.2          munsell_0.4.3              gtable_0.2.0               mvtnorm_1.0-5             
[17] irlba_2.0.0                Rcpp_0.12.6                scales_0.4.0               plotrix_3.6-3             
[21] scatterplot3d_0.3-37       graph_1.50.0               XVector_0.12.1             Rsamtools_1.24.0          
[25] png_0.1-7                  Rtsne_0.11                 tools_3.3.0                RSQLite_1.0.0             
[29] pheatmap_1.0.8             httr_1.2.1                 pixmap_0.4-11              R6_2.1.3                  
[33] GenomicAlignments_1.8.4

biomaRt • 1.5k views

ADD COMMENT • link updated 8.3 years ago by Laurent Gatto 1.6k • written 8.3 years ago by rubi ▴ 110

score 0 · Answer 1 · 2016-08-28

Hello, Are you using the main Ensembl site as your BioMart host? If so please note that the Ensembl site is currently down due to data centre maintenance (http://www.ensembl.org/index.html). You can use one of our mirror sites asia.ensembl.org, uswest.ensembl.org, useast.ensembl.org) for your biomaRt queries. Ive tried uswest.ensembl.org with the example commands below and it works. We are expecting the main Ensembl site to be fully up and running by afternoon (GMT) of Tuesday 30 August. Please let us know if you encounter connecting to any of the mirror sites. Best regards, Amonida Example commands ** uswest_mouse=useMart(host='uswest.ensembl.org',biomart='ENSEMBL_MART_ENSEMBL',dataset='mmusculus_gene_ensembl') > head(listDatasets(uswest_mouse)) dataset description version 1 oanatinus_gene_ensembl Ornithorhynchus anatinus genes (OANA5) OANA5 2 cporcellus_gene_ensembl Cavia porcellus genes (cavPor3) cavPor3 3 gaculeatus_gene_ensembl Gasterosteus aculeatus genes (BROADS1) BROADS1 4 itridecemlineatus_gene_ensembl Ictidomys tridecemlineatus genes (spetri2) spetri2 5 lafricana_gene_ensembl Loxodonta africana genes (loxAfr3) loxAfr3 6 choffmanni_gene_ensembl Choloepus hoffmanni genes (choHof1) choHof1 > head(listFilters(uswest_mouse)) name description 1 chromosome_name Chromosome name 2 start Gene Start (bp) 3 end Gene End (bp) 4 band_start Band Start 5 band_end Band End 6 marker_start Marker Start chr1_genes <- getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id','mgi_symbol','chromosome_name','start_position','end_position'), filters = 'chromosome_name', values ="1", mart = uswest_mouse) > head(chr1_genes) ensembl_gene_id ensembl_transcript_id mgi_symbol chromosome_name start_position end_position 1 ENSMUSG00000065192 ENSMUST00000083258 Gm23460 1 52444436 52444544 2 ENSMUSG00000065160 ENSMUST00000083226 Mir5117 1 161037356 161037439 3 ENSMUSG00000088333 ENSMUST00000157708 Gm27396 1 3783876 3783933 4 ENSMUSG00000088829 ENSMUST00000158204 Gm25227 1 15685935 15686046 5 ENSMUSG00000099208 ENSMUST00000184449 Gm27940 1 195240910 195241007 6 ENSMUSG00000096297 ENSMUST00000179111 Gm23934 1 80135466 80135572 -- Amonida Zadissa Ensembl Prodcuction EMBL-EBI Hinxton England On 27/08/2016 21:06, rubi [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User rubi <https: support.bioconductor.org="" u="" 6462=""/> wrote Question: Error: 1: > Extra content at the end of the document in using biomaRt > <https: support.bioconductor.org="" p="" 86554=""/>: > > Hi, > > I'm trying to get mouse Entrez IDs of Ensembl IDs and thought that using biomaRt > will be the right thing to do. > > So I installed biomaRt and trying to run: > >> mart <- useMart(biomart="ensembl", dataset="mmusculus_gene_ensembl") > > or > >> listEnsembl() > > I'm getting this error: > > Extra content at the end of the document > Error: 1: Extra content at the end of the document > > Help would be appreciated > > <font face="sans-serif, Arial, Verdana, Trebuchet MS"> > sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-redhat-linux-gnu > (64-bit) Running under: CentOS Linux 7 (Core) locale: [1] LC_CTYPE=en_US.UTF-8 > LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > attached base packages: [1] tcltk grid stats4 parallel stats graphics grDevices > utils datasets methods base other attached packages: [1] RCurl_1.95-4.8 > bitops_1.0-6 [3] biomaRt_2.28.0 BiocInstaller_1.22.3 [5] PCGSE_0.2 MASS_7.3-45 > [7] RMTstat_0.3 safe_3.12.0 [9] SparseM_1.7 data.table_1.9.6 [11] asbio_1.3-4 > gridExtra_2.2.1 [13] org.Mm.eg.db_3.3.0 TxDb.Mmusculus.UCSC.mm10.ensGene_3.2.2 > [15] GenomicFeatures_1.24.5 AnnotationDbi_1.34.4 [17] GenomicRanges_1.24.2 > GenomeInfoDb_1.8.3 [19] IRanges_2.6.1 S4Vectors_0.10.3 [21] gageData_2.10.0 > gage_2.22.0 [23] cellrangerRkit_0.99.0 Rmisc_1.5 [25] plyr_1.8.4 lattice_0.20-33 > [27] bit64_0.9-5 bit_1.1-12 [29] ggplot2_2.1.0 RColorBrewer_1.1-2 [31] > Biobase_2.32.0 BiocGenerics_0.18.0 [33] Matrix_1.2-6 loaded via a namespace (and > not attached): [1] deSolve_1.13 KEGGREST_1.12.2 SummarizedExperiment_1.2.3 > rhdf5_2.16.0 [5] colorspace_1.2-6 rtracklayer_1.32.2 chron_2.3-47 XML_3.98-1.4 > [9] DBI_0.5 BiocParallel_1.6.6 multcompView_0.1-7 zlibbioc_1.18.0 [13] > Biostrings_2.40.2 munsell_0.4.3 gtable_0.2.0 mvtnorm_1.0-5 [17] irlba_2.0.0 > Rcpp_0.12.6 scales_0.4.0 plotrix_3.6-3 [21] scatterplot3d_0.3-37 graph_1.50.0 > XVector_0.12.1 Rsamtools_1.24.0 [25] png_0.1-7 Rtsne_0.11 tools_3.3.0 > RSQLite_1.0.0 [29] pheatmap_1.0.8 httr_1.2.1 pixmap_0.4-11 R6_2.1.3 [33] > GenomicAlignments_1.8.4 </font> > > -------------------------------------------------------------------------------- > > Post tags: biomaRt > > You may reply via email or visit Error: 1: Extra content at the end of the document in using biomaRt >

score 0 · Answer 2 · 2016-08-28

I assume this is related to the maintenance downtime. I also get

> biomaRt::listMarts(verbose = TRUE)
Attempting web service request:
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Extra content at the end of the document
Error: 1: Extra content at the end of the document

and, if I browse to www.ensembl.org

Due to essential Data Centre maintenance, the Ensembl web service will be unavailable from 14:00 BST on Friday 26th August 2016 BST until 11:00 BST on Tuesday 30th August 2016.

If you require further information please visit our Status blog.

The Ensembl web service you requested is temporarily unavailable. We are working to restore the service as soon as possible. We apologise for any inconvenience caused.