Tonight I suddenly got the following database error:

Error in getBM(c(seqType, type), filters = type, values = id, mart = mart,  : 
  Query ERROR: caught BioMart::Exception::Database: Error during query execution: Can't find file: './ensembl_mart_55/hsapiens_gene_ensembl__exon_transcript__dm.frm' (errno: 13)

I usually start a connection through the following command:

hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl'

Since the above error message  looks like another user's database exception, I tried out the suggestion that was provided by Bioconductor experts for that case. Unluckily it doesn't work for me as shown in the following run log excerpt.
Is there anything I can do other than wait & hope ?
Thank you in advance,
Maura 

> hmart <- useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host="www.ensembl.org")
Checking attributes ... ok
Checking filters ... ok
> gene.map <- getBM (attributes=c("hgnc_symbol","ensembl_gene_id","ensembl_transcript_id"),
+ filters = "ensembl_gene_id", values = "ENSG00000162599", mart=hmart)
> gene.map
  hgnc_symbol ensembl_gene_id ensembl_transcript_id
1        NFIA ENSG00000162599       ENST00000371191
2        NFIA ENSG00000162599       ENST00000407417
3        NFIA ENSG00000162599       ENST00000401818
4        NFIA ENSG00000162599       ENST00000403491
5        NFIA ENSG00000162599       ENST00000357977
6        NFIA ENSG00000162599       ENST00000371189
7        NFIA ENSG00000162599       ENST00000371185
8        NFIA ENSG00000162599       ENST00000371184
9        NFIA ENSG00000162599       ENST00000371187
> gene.seq <- getSequence (id=gene.map[,"ensembl_transcript_id"], type="ensembl_transcript_id", seqType="3utr",mart=hmart)
Error in martCheck(mart, "ensembl") : 
  This function only works when used with the ensembl BioMart.
> hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl')
Checking attributes ... ok
Checking filters ... ok
> gene.seq <- getSequence (id=gene.map[,"ensembl_transcript_id"], type="ensembl_transcript_id", seqType="3utr",mart=hmart)
Error in getBM(c(seqType, type), filters = type, values = id, mart = mart,  : 
  Query ERROR: caught BioMart::Exception::Database: Error during query execution: Can't find file: './ensembl_mart_55/hsapiens_gene_ensembl__exon_transcript__dm.frm' (errno: 13)




tutti i telefonini TIM!


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