Hi,
Do you permission to write inside /mnt/ephemeral0/mysqltmp/?
Regards,
Pascal
On 05/07/2013 06:41 PM, Mohammad Tanvir Ahamed 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
>
> [[alternative HTML version deleted]]
>
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>