R help - May 2013 - Problem with biomaRt::getSequence.

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]]

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]]
>
>
>
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