Hi, I can run the code some days ago . But cant run now. Problem 1: Output is ok ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) utr5 = getSequence(chromosome=3, start=185514033, end=185535839, type="entrezgene",seqType="5utr", mart=ensembl) Output : 5utr entrezgene Sequence unavailable 10644 GGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG 10644 3 GGGGGGCGGAGGAGGAGGAGAGACGAGGGCAGCGGAGGAGGCGAGGAGCGCCGGGTACCGGGCCGGGG GAGCCGCGGGCTCTCGGGGAAGAGACGG 10644 CGGAGGAGGCGAGGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG 10644 No UTR is annotated for this transcript 10644 Problem 2:Problem is here protein = getSequence(id=c(100, 5728),type="entrezgene",seqType="peptide", mart=ensembl) Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, : Query ERROR: caught BioMart::Exception::Database: Error during query execution: Can't create/write to file '/mnt/ephemeral0/mysqltmp/#sql_40a_0.MYI' (Errcode: 2) I need help please. -- output of sessionInfo(): R version 3.0.0 (2013-04-03) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Bangla_Bangladesh.1252 LC_CTYPE=Bangla_Bangladesh.1252 LC_MONETARY=Bangla_Bangladesh.1252 LC_NUMERIC=C [5] LC_TIME=Bangla_Bangladesh.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] seqinr_3.0-7 biomaRt_2.16.0 loaded via a namespace (and not attached): [1] RCurl_1.95-4.1 tools_3.0.0 XML_3.96-1.1 -- Sent via the guest posting facility at bioconductor.org.

On Tue, May 7, 2013 at 6:54 AM, Tanvir Ahamed [guest] <guest at="" bioconductor.org=""> wrote: > > Hi, > I can run the code some days ago . But cant run now. > > Problem 1: Output is ok > ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) > utr5 = getSequence(chromosome=3, start=185514033, end=185535839, type="entrezgene",seqType="5utr", mart=ensembl) > Output : > 5utr entrezgene > Sequence unavailable 10644 > GGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG 10644 > 3 GGGGGGCGGAGGAGGAGGAGAGACGAGGGCAGCGGAGGAGGCGAGGAGCGCCGGGTACCGGGCCGG GGGAGCCGCGGGCTCTCGGGGAAGAGACGG 10644 > CGGAGGAGGCGAGGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG 10644 > No UTR is annotated for this transcript 10644 > > Problem 2:Problem is here > protein = getSequence(id=c(100, 5728),type="entrezgene",seqType="peptide", mart=ensembl) > > Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, : > Query ERROR: caught BioMart::Exception::Database: Error during query execution: Can't create/write to file '/mnt/ephemeral0/mysqltmp/#sql_40a_0.MYI' (Errcode: 2) This is most likely a problem on the machine that is running the biomart (presumably Ensembl). I suspect that they'll pick up on this by themselves, so try your query in a little bit to see if the problem has been fixed. If it is not resolved, I'd suggesting writing to the biomart folks at ensembl. I do not think this is something you are doing wrong or that there is anything you can do yourself to fix it. Sean > I need help please. > > > -- output of sessionInfo(): > > R version 3.0.0 (2013-04-03) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=Bangla_Bangladesh.1252 LC_CTYPE=Bangla_Bangladesh.1252 LC_MONETARY=Bangla_Bangladesh.1252 LC_NUMERIC=C > [5] LC_TIME=Bangla_Bangladesh.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] seqinr_3.0-7 biomaRt_2.16.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.95-4.1 tools_3.0.0 XML_3.96-1.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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