Problems accessing Ensembl archive 59 with EnsEMBL
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Aedin Culhane ▴ 510
@aedin-culhane-1526
Last seen 4.5 years ago
United States
Dear BioC Users (and Steffen) Whilst my script is working successfully to access older archives of EnsEMBL, I can't access EnsEMBL 59. I'd be grateful if you could help me determine what the problem is. Whilst useMart works, listDatasets return no datasets in EnsEMBL59 mart. #---------- #EnsEMBL Archive URLS #----------- urls= list( EnsEMBL57= "mar2010.archive.ensembl.org", EnsEMBL58= "may2010.archive.ensembl.org", EnsEMBL59= "aug2010.archive.ensembl.org") #---------- #Quick Check Script to see problem with EnsEMBL 59 #----------- for (EnsEMBLarchiveURL in urls) { print(EnsEMBLarchiveURL) ## Quick check marts ok print(listMarts(host=EnsEMBLarchiveURL,path="/biomart/martservice",arc hive=FALSE)[1:2,]) mart = useMart("ENSEMBL_MART_ENSEMBL", host=EnsEMBLarchiveURL,path="/biomart/martservice",archive=FALSE) datasets <- listDatasets(mart) ## Quick check datasets ok print(dim(datasets)) } mart<-useDataset("hsapiens_gene_ensembl",mart) [1] "mar2010.archive.ensembl.org" biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 57 2 ENSEMBL_MART_SNP Ensembl Variation 57 [1] 51 3 [1] "may2010.archive.ensembl.org" biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 58 2 ENSEMBL_MART_SNP Ensembl Variation 58 [1] 51 3 [1] "aug2010.archive.ensembl.org" biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 59 2 ENSEMBL_MART_SNP Ensembl Variation 59 [1] 0 3 > > mart<-useDataset("hsapiens_gene_ensembl",mart) Error in useDataset("hsapiens_gene_ensembl", mart) : The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets function. Thanks a million Aedin > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i486-pc-linux-gnu (32-bit) 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=C 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_2.6.0 loaded via a namespace (and not attached): [1] RCurl_1.4-3 tools_2.12.0 XML_3.2-0
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@rhoda-kinsella-3200
Last seen 9.6 years ago
Hi Aedin The host name in the registry is incorrect. I have reported this issue to the Ensembl webteam and we will try to fix it as soon as possible. Thank you for reporting this and apologies for any inconvenience. Rhoda On 1 Dec 2010, at 21:21, aedin culhane wrote: > Dear BioC Users (and Steffen) > Whilst my script is working successfully to access older archives of > EnsEMBL, I can't access EnsEMBL 59. I'd be grateful if you could > help me determine what the problem is. Whilst useMart works, > listDatasets return no datasets in EnsEMBL59 mart. > > #---------- > #EnsEMBL Archive URLS > #----------- > urls= list( EnsEMBL57= "mar2010.archive.ensembl.org", > EnsEMBL58= "may2010.archive.ensembl.org", > EnsEMBL59= "aug2010.archive.ensembl.org") > > > > #---------- > #Quick Check Script to see problem with EnsEMBL 59 > #----------- > for (EnsEMBLarchiveURL in urls) { > print(EnsEMBLarchiveURL) > > ## Quick check marts ok > print(listMarts(host=EnsEMBLarchiveURL,path="/biomart/ > martservice",archive=FALSE)[1:2,]) > > > mart = useMart("ENSEMBL_MART_ENSEMBL", > host=EnsEMBLarchiveURL,path="/biomart/martservice",archive=FALSE) > datasets <- listDatasets(mart) > > ## Quick check datasets ok > print(dim(datasets)) > } > > mart<-useDataset("hsapiens_gene_ensembl",mart) > > > [1] "mar2010.archive.ensembl.org" > biomart version > 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 57 > 2 ENSEMBL_MART_SNP Ensembl Variation 57 > [1] 51 3 > [1] "may2010.archive.ensembl.org" > biomart version > 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 58 > 2 ENSEMBL_MART_SNP Ensembl Variation 58 > [1] 51 3 > [1] "aug2010.archive.ensembl.org" > biomart version > 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 59 > 2 ENSEMBL_MART_SNP Ensembl Variation 59 > [1] 0 3 > > > > mart<-useDataset("hsapiens_gene_ensembl",mart) > Error in useDataset("hsapiens_gene_ensembl", mart) : > The given dataset: hsapiens_gene_ensembl , is not valid. Correct > dataset names can be obtained with the listDatasets function. > > > > Thanks a million > Aedin > > > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i486-pc-linux-gnu (32-bit) > > 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=C 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_2.6.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.4-3 tools_2.12.0 XML_3.2-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
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Hi Rhonda Thanks for your reply. Can I use a different URL in the interim? Aedin On 12/02/2010 04:16 AM, Rhoda Kinsella wrote: > Hi Aedin > The host name in the registry is incorrect. I have reported this issue > to the Ensembl webteam and we will try to fix it as soon as possible. > Thank you for reporting this and apologies for any inconvenience. > Rhoda > > On 1 Dec 2010, at 21:21, aedin culhane wrote: > >> Dear BioC Users (and Steffen) >> Whilst my script is working successfully to access older archives of >> EnsEMBL, I can't access EnsEMBL 59. I'd be grateful if you could help >> me determine what the problem is. Whilst useMart works, listDatasets >> return no datasets in EnsEMBL59 mart. >> >> #---------- >> #EnsEMBL Archive URLS >> #----------- >> urls= list( EnsEMBL57= "mar2010.archive.ensembl.org", >> EnsEMBL58= "may2010.archive.ensembl.org", >> EnsEMBL59= "aug2010.archive.ensembl.org") >> >> >> >> #---------- >> #Quick Check Script to see problem with EnsEMBL 59 >> #----------- >> for (EnsEMBLarchiveURL in urls) { >> print(EnsEMBLarchiveURL) >> >> ## Quick check marts ok >> print(listMarts(host=EnsEMBLarchiveURL,path="/biomart/martservice", archive=FALSE)[1:2,]) >> >> >> >> mart = useMart("ENSEMBL_MART_ENSEMBL", >> host=EnsEMBLarchiveURL,path="/biomart/martservice",archive=FALSE) >> datasets <- listDatasets(mart) >> >> ## Quick check datasets ok >> print(dim(datasets)) >> } >> >> mart<-useDataset("hsapiens_gene_ensembl",mart) >> >> >> [1] "mar2010.archive.ensembl.org" >> biomart version >> 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 57 >> 2 ENSEMBL_MART_SNP Ensembl Variation 57 >> [1] 51 3 >> [1] "may2010.archive.ensembl.org" >> biomart version >> 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 58 >> 2 ENSEMBL_MART_SNP Ensembl Variation 58 >> [1] 51 3 >> [1] "aug2010.archive.ensembl.org" >> biomart version >> 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 59 >> 2 ENSEMBL_MART_SNP Ensembl Variation 59 >> [1] 0 3 >> > >> > mart<-useDataset("hsapiens_gene_ensembl",mart) >> Error in useDataset("hsapiens_gene_ensembl", mart) : >> The given dataset: hsapiens_gene_ensembl , is not valid. Correct >> dataset names can be obtained with the listDatasets function. >> >> >> >> Thanks a million >> Aedin >> >> >> >> > sessionInfo() >> R version 2.12.0 (2010-10-15) >> Platform: i486-pc-linux-gnu (32-bit) >> >> 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=C 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_2.6.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.4-3 tools_2.12.0 XML_3.2-0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > Rhoda Kinsella Ph.D. > Ensembl Bioinformatician, > European Bioinformatics Institute (EMBL-EBI), > Wellcome Trust Genome Campus, > Hinxton > Cambridge CB10 1SD, > UK. >
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Hi Aedin, I'm afraid not but you can of course link to the current release 60 on www.ensembl.org or www.biomart.org. The web team have assured me they will fix it as soon as possible. Regards, Rhoda On 2 Dec 2010, at 15:20, aedin culhane wrote: > Hi Rhonda > Thanks for your reply. Can I use a different URL in the interim? > Aedin > > On 12/02/2010 04:16 AM, Rhoda Kinsella wrote: >> Hi Aedin >> The host name in the registry is incorrect. I have reported this >> issue >> to the Ensembl webteam and we will try to fix it as soon as possible. >> Thank you for reporting this and apologies for any inconvenience. >> Rhoda >> >> On 1 Dec 2010, at 21:21, aedin culhane wrote: >> >>> Dear BioC Users (and Steffen) >>> Whilst my script is working successfully to access older archives of >>> EnsEMBL, I can't access EnsEMBL 59. I'd be grateful if you could >>> help >>> me determine what the problem is. Whilst useMart works, listDatasets >>> return no datasets in EnsEMBL59 mart. >>> >>> #---------- >>> #EnsEMBL Archive URLS >>> #----------- >>> urls= list( EnsEMBL57= "mar2010.archive.ensembl.org", >>> EnsEMBL58= "may2010.archive.ensembl.org", >>> EnsEMBL59= "aug2010.archive.ensembl.org") >>> >>> >>> >>> #---------- >>> #Quick Check Script to see problem with EnsEMBL 59 >>> #----------- >>> for (EnsEMBLarchiveURL in urls) { >>> print(EnsEMBLarchiveURL) >>> >>> ## Quick check marts ok >>> print(listMarts(host=EnsEMBLarchiveURL,path="/biomart/ >>> martservice",archive=FALSE)[1:2,]) >>> >>> >>> >>> mart = useMart("ENSEMBL_MART_ENSEMBL", >>> host=EnsEMBLarchiveURL,path="/biomart/martservice",archive=FALSE) >>> datasets <- listDatasets(mart) >>> >>> ## Quick check datasets ok >>> print(dim(datasets)) >>> } >>> >>> mart<-useDataset("hsapiens_gene_ensembl",mart) >>> >>> >>> [1] "mar2010.archive.ensembl.org" >>> biomart version >>> 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 57 >>> 2 ENSEMBL_MART_SNP Ensembl Variation 57 >>> [1] 51 3 >>> [1] "may2010.archive.ensembl.org" >>> biomart version >>> 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 58 >>> 2 ENSEMBL_MART_SNP Ensembl Variation 58 >>> [1] 51 3 >>> [1] "aug2010.archive.ensembl.org" >>> biomart version >>> 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 59 >>> 2 ENSEMBL_MART_SNP Ensembl Variation 59 >>> [1] 0 3 >>> > >>> > mart<-useDataset("hsapiens_gene_ensembl",mart) >>> Error in useDataset("hsapiens_gene_ensembl", mart) : >>> The given dataset: hsapiens_gene_ensembl , is not valid. Correct >>> dataset names can be obtained with the listDatasets function. >>> >>> >>> >>> Thanks a million >>> Aedin >>> >>> >>> >>> > sessionInfo() >>> R version 2.12.0 (2010-10-15) >>> Platform: i486-pc-linux-gnu (32-bit) >>> >>> 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=C 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_2.6.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_1.4-3 tools_2.12.0 XML_3.2-0 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> Rhoda Kinsella Ph.D. >> Ensembl Bioinformatician, >> European Bioinformatics Institute (EMBL-EBI), >> Wellcome Trust Genome Campus, >> Hinxton >> Cambridge CB10 1SD, >> UK. >> Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
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