biomart package - error querying for ensembl gene ID in snp mart

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Rhoda Kinsella ▴ 660

@rhoda-kinsella-3200

Last seen 9.7 years ago

Hi Martin, I will report your error to mart-dev@ebi.ac.uk. This is the e-mail list you should use to report errors relating to the www.biomart.org martview and martservice. Unfortunately, you cannot access the ensembl server using the BiomaRt package at the moment as there has been an error in the registry. We plan to rectify this for the forthcoming release due at the beginning of March. I think you should use the ensembl.org mart interface or the martservice until the bug is fixed. I hope that helps, Regards, Rhoda On 25 Feb 2009, at 11:05, martin sikora wrote: > hi rhoda, > > thanks for the reply! i have found out that this error does only > occur when you use the central biomart server, directly at ensembl > it works, as you have shown. you can see the error in the > screenshots, the one without Ensembl Gene ID works fine, but once i > add it i get the same error as with using the biomaRt package. is > there a way to use the ensembl server instead in the package? > > cheers > martin > > Rhoda Kinsella schrieb: >> >> Apologies if you have already received this message. I had a bounce >> back message from the >> Bioconductor mailing list so I thought I should re-send, just in >> case... >> >> >> Hi Martin, >> I have looked into this and I can't seem to reproduce the error >> using the webservice (see screenshot). >> Can you send me a screen shot of the mart web interface query that >> you performed along with the >> error that you get from the web interface? >> Regards, >> Rhoda >> >> >> >> <mime-attachment.jpeg> >> >> >> >> On 24 Feb 2009, at 22:33, martin sikora wrote: >> >>> ok, so i seem to get the same error on the biomart web-service, so >>> definitely some problem of the database.. >>> >>> thanks anyways, >>> >>> cheers >>> martin >>> >>> martin sikora schrieb: >>>> dear all, >>>> >>>> i am getting an error trying to retrieve some attributes from the >>>> variation biomart at ensembl (see code below). so far i got this >>>> error >>>> only when trying to retrieve either ensembl gene or transcript >>>> IDs for >>>> a certain SNP. other queries like alleles etc seem to work fine. >>>> maybe >>>> some changes at the biomart server for these attributes? >>>> >>>> cheers >>>> martin >>>> >>>> --- >>>> >>>>> library( biomaRt ) >>>>> snp129Mart <- useMart( "snp", dataset = "hsapiens_snp" ) >>>> Checking attributes and filters ... ok >>>>> getBM( attributes = c( "ensembl_gene_stable_id"), filter = >>>>> "refsnp", >>>> "rs10399749", mart = snp129Mart ) >>>> >>>> ensembl_gene_stable_id >>>> 1 Query ERROR: caught BioMart::Exception::Database: Error during >>>> query >>>> execution: File >>>> './snp_mart_52/hsapiens_snp__transcript_variation__dm.MYD' not >>>> found >>>> (Errcode: 27) >>>> >>>> >>>>> sessionInfo() >>>> >>>> R version 2.8.1 Patched (2009-01-19 r47650) >>>> i386-apple-darwin9.6.0 >>>> >>>> locale: >>>> C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices datasets utils methods >>>> base >>>> >>>> other attached packages: >>>> [1] biomaRt_1.16.0 R.utils_1.1.1 R.oo_1.4.6 >>>> R.methodsS3_1.0.3 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] RCurl_0.94-1 XML_2.1-0 tools_2.8.1 >>>> >>>> >>>> -- >>>> :: martin sikora >>>> :: IBE, institut de biologia evolutiva (UPF-CSIC) >>>> :: CEXS-UPF-PRBB >>>> :: doctor aiguader 88, 08003 barcelona >>>> >>>> :: tel. (+34) 93 316 0802 >>>> :: martin.sikora@upf.edu <mailto:martin.sikora@upf.edu> >>> >>> >>> -- >>> :: martin sikora >>> :: IBE, institut de biologia evolutiva (UPF-CSIC) >>> :: CEXS-UPF-PRBB >>> :: doctor aiguader 88, 08003 barcelona >>> >>> :: tel. (+34) 93 316 0802 >>> :: martin.sikora@upf.edu <mailto:martin.sikora@upf.edu> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> 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. >> > > > -- > :: martin sikora > :: IBE, institut de biologia evolutiva (UPF-CSIC) > :: CEXS-UPF-PRBB > :: doctor aiguader 88, 08003 barcelona > > :: tel. (+34) 93 316 0802 > :: martin.sikora@upf.edu > <error.png><noerror.png> Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. [[alternative HTML version deleted]]

SNP biomaRt SNP biomaRt • 806 views

ADD COMMENT • link 15.2 years ago Rhoda Kinsella ▴ 660

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Entering edit mode

Rhoda Kinsella ▴ 660

@rhoda-kinsella-3200

Last seen 9.7 years ago

Hi Martin, It seems there were problems with the martdb.ensembl.org server. This issue has been fixed and you should be able to carry out your query now. Apologies for any inconvenience. Regards, Rhoda On 25 Feb 2009, at 11:05, martin sikora wrote: > hi rhoda, > > thanks for the reply! i have found out that this error does only > occur when you use the central biomart server, directly at ensembl > it works, as you have shown. you can see the error in the > screenshots, the one without Ensembl Gene ID works fine, but once i > add it i get the same error as with using the biomaRt package. is > there a way to use the ensembl server instead in the package? > > cheers > martin > > Rhoda Kinsella schrieb: >> >> Apologies if you have already received this message. I had a bounce >> back message from the >> Bioconductor mailing list so I thought I should re-send, just in >> case... >> >> >> Hi Martin, >> I have looked into this and I can't seem to reproduce the error >> using the webservice (see screenshot). >> Can you send me a screen shot of the mart web interface query that >> you performed along with the >> error that you get from the web interface? >> Regards, >> Rhoda >> >> >> >> <mime-attachment.jpeg> >> >> >> >> On 24 Feb 2009, at 22:33, martin sikora wrote: >> >>> ok, so i seem to get the same error on the biomart web-service, so >>> definitely some problem of the database.. >>> >>> thanks anyways, >>> >>> cheers >>> martin >>> >>> martin sikora schrieb: >>>> dear all, >>>> >>>> i am getting an error trying to retrieve some attributes from the >>>> variation biomart at ensembl (see code below). so far i got this >>>> error >>>> only when trying to retrieve either ensembl gene or transcript >>>> IDs for >>>> a certain SNP. other queries like alleles etc seem to work fine. >>>> maybe >>>> some changes at the biomart server for these attributes? >>>> >>>> cheers >>>> martin >>>> >>>> --- >>>> >>>>> library( biomaRt ) >>>>> snp129Mart <- useMart( "snp", dataset = "hsapiens_snp" ) >>>> Checking attributes and filters ... ok >>>>> getBM( attributes = c( "ensembl_gene_stable_id"), filter = >>>>> "refsnp", >>>> "rs10399749", mart = snp129Mart ) >>>> >>>> ensembl_gene_stable_id >>>> 1 Query ERROR: caught BioMart::Exception::Database: Error during >>>> query >>>> execution: File >>>> './snp_mart_52/hsapiens_snp__transcript_variation__dm.MYD' not >>>> found >>>> (Errcode: 27) >>>> >>>> >>>>> sessionInfo() >>>> >>>> R version 2.8.1 Patched (2009-01-19 r47650) >>>> i386-apple-darwin9.6.0 >>>> >>>> locale: >>>> C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices datasets utils methods >>>> base >>>> >>>> other attached packages: >>>> [1] biomaRt_1.16.0 R.utils_1.1.1 R.oo_1.4.6 >>>> R.methodsS3_1.0.3 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] RCurl_0.94-1 XML_2.1-0 tools_2.8.1 >>>> >>>> >>>> -- >>>> :: martin sikora >>>> :: IBE, institut de biologia evolutiva (UPF-CSIC) >>>> :: CEXS-UPF-PRBB >>>> :: doctor aiguader 88, 08003 barcelona >>>> >>>> :: tel. (+34) 93 316 0802 >>>> :: martin.sikora@upf.edu <mailto:martin.sikora@upf.edu> >>> >>> >>> -- >>> :: martin sikora >>> :: IBE, institut de biologia evolutiva (UPF-CSIC) >>> :: CEXS-UPF-PRBB >>> :: doctor aiguader 88, 08003 barcelona >>> >>> :: tel. (+34) 93 316 0802 >>> :: martin.sikora@upf.edu <mailto:martin.sikora@upf.edu> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> 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. >> > > > -- > :: martin sikora > :: IBE, institut de biologia evolutiva (UPF-CSIC) > :: CEXS-UPF-PRBB > :: doctor aiguader 88, 08003 barcelona > > :: tel. (+34) 93 316 0802 > :: martin.sikora@upf.edu > <error.png><noerror.png> Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. [[alternative HTML version deleted]]

ADD COMMENT • link 15.2 years ago Rhoda Kinsella ▴ 660

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hi rhoda, i can confirm it's working now! thanks again, cheers martin Rhoda Kinsella schrieb: > Hi Martin, > It seems there were problems with the martdb.ensembl.org server. This > issue has been fixed and you should be able to carry out your query > now. Apologies for any inconvenience. > Regards, > Rhoda > > > On 25 Feb 2009, at 11:05, martin sikora wrote: > >> hi rhoda, >> >> thanks for the reply! i have found out that this error does only >> occur when you use the central biomart server, directly at ensembl it >> works, as you have shown. you can see the error in the screenshots, >> the one without Ensembl Gene ID works fine, but once i add it i get >> the same error as with using the biomaRt package. is there a way to >> use the ensembl server instead in the package? >> >> cheers >> martin >> >> Rhoda Kinsella schrieb: >>> Apologies if you have already received this message. I had a bounce >>> back message from the >>> Bioconductor mailing list so I thought I should re-send, just in >>> case... >>> >>> >>> Hi Martin, >>> I have looked into this and I can't seem to reproduce the error >>> using the webservice (see screenshot). >>> Can you send me a screen shot of the mart web interface query that >>> you performed along with the >>> error that you get from the web interface? >>> Regards, >>> Rhoda >>> >>> >>> ------------------------------------------------------------------ ------ >>> >>> <mime-attachment.jpeg> >>> >>> >>> >>> >>> On 24 Feb 2009, at 22:33, martin sikora wrote: >>> >>>> ok, so i seem to get the same error on the biomart web-service, so >>>> definitely some problem of the database.. >>>> >>>> thanks anyways, >>>> >>>> cheers >>>> martin >>>> >>>> martin sikora schrieb: >>>>> dear all, >>>>> >>>>> i am getting an error trying to retrieve some attributes from the >>>>> variation biomart at ensembl (see code below). so far i got this >>>>> error >>>>> only when trying to retrieve either ensembl gene or transcript IDs >>>>> for >>>>> a certain SNP. other queries like alleles etc seem to work fine. >>>>> maybe >>>>> some changes at the biomart server for these attributes? >>>>> >>>>> cheers >>>>> martin >>>>> >>>>> --- >>>>> >>>>>> library( biomaRt ) >>>>>> snp129Mart <- useMart( "snp", dataset = "hsapiens_snp" ) >>>>> Checking attributes and filters ... ok >>>>>> getBM( attributes = c( "ensembl_gene_stable_id"), filter = "refsnp", >>>>> "rs10399749", mart = snp129Mart ) >>>>> >>>>> ensembl_gene_stable_id >>>>> 1 Query ERROR: caught BioMart::Exception::Database: Error during >>>>> query >>>>> execution: File >>>>> './snp_mart_52/hsapiens_snp__transcript_variation__dm.MYD' not found >>>>> (Errcode: 27) >>>>> >>>>> >>>>>> sessionInfo() >>>>> >>>>> R version 2.8.1 Patched (2009-01-19 r47650) >>>>> i386-apple-darwin9.6.0 >>>>> >>>>> locale: >>>>> C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices datasets utils methods base >>>>> >>>>> other attached packages: >>>>> [1] biomaRt_1.16.0 R.utils_1.1.1 R.oo_1.4.6 >>>>> R.methodsS3_1.0.3 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] RCurl_0.94-1 XML_2.1-0 tools_2.8.1 >>>>> >>>>> >>>>> -- >>>>> :: martin sikora >>>>> :: IBE, institut de biologia evolutiva (UPF-CSIC) >>>>> :: CEXS-UPF-PRBB >>>>> :: doctor aiguader 88, 08003 barcelona >>>>> >>>>> :: tel. (+34) 93 316 0802 >>>>> :: martin.sikora@upf.edu <mailto:martin.sikora@upf.edu> >>>> >>>> >>>> -- >>>> :: martin sikora >>>> :: IBE, institut de biologia evolutiva (UPF-CSIC) >>>> :: CEXS-UPF-PRBB >>>> :: doctor aiguader 88, 08003 barcelona >>>> >>>> :: tel. (+34) 93 316 0802 >>>> :: martin.sikora@upf.edu <mailto:martin.sikora@upf.edu> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@stat.math.ethz.ch >>>> 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. >>> >> >> >> -- >> :: martin sikora >> :: IBE, institut de biologia evolutiva (UPF-CSIC) >> :: CEXS-UPF-PRBB >> :: doctor aiguader 88, 08003 barcelona >> >> :: tel. (+34) 93 316 0802 >> :: martin.sikora@upf.edu <mailto:martin.sikora@upf.edu> >> <error.png><noerror.png> > > Rhoda Kinsella Ph.D. > Ensembl Bioinformatician, > European Bioinformatics Institute (EMBL-EBI), > Wellcome Trust Genome Campus, > Hinxton > Cambridge CB10 1SD, > UK. > -- :: martin sikora :: IBE, institut de biologia evolutiva (UPF-CSIC) :: CEXS-UPF-PRBB :: doctor aiguader 88, 08003 barcelona :: tel. (+34) 93 316 0802 :: martin.sikora@upf.edu <mailto:martin.sikora@upf.edu> [[alternative HTML version deleted]]

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