[ensembl-dev] Problem with biomaRt::getSequence

[Mohammad Tanvir Ahamed]

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
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