Hi list, I included the actual XML query that results in the error Mohammad is reporting:
The query: <?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= "biomaRt"> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'peptide'/><Attribute name = 'entrezgene'/><Filter name = 'entrezgene' value = '100,5728' /></Dataset></Query> gives: caught BioMart::Exception::Database: Error during query execution: Can't create/write to file '/mnt/ephemeral0/mysqltmp/#sql_40a_0.MYI' (Errcode: 2) This comes from the central BioMart server (www.biomart.org), can anyone help? Best, Steffen On Wed, May 8, 2013 at 5:27 AM, Mohammad Tanvir Ahamed <[email protected]>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 > GGGGGGCGGAGGAGGAGGAGAGACGAGGGCAGCGGAGGAGGCGAGGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG > 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 > > */.......Tanvir Ahamed* > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users >
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