[R] Problem with biomaRt::getSequence.

[Pascal Oettli]

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
>
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>
>
>
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