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 -------------- next part -------------- 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 at upf.edu <mailto:martin.sikora at="" 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 at upf.edu <mailto:martin.sikora at="" upf.edu=""> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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.

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 -------------- next part -------------- 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 at upf.edu <mailto:martin.sikora at="" 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 at upf.edu <mailto:martin.sikora at="" upf.edu=""> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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.