[BioC] error in getBM ... Query ERROR: caught BioMart::Exception:

mauede at alice.it mauede at alice.it
Thu Jul 2 14:29:07 CEST 2009

I am getting the following error upon execution of the following instruction during the first loop iteration:

> for(j in 1:nrow(gene.map)) {
+ seq <- ""
+ seq = getSequence(id=gene.map[j,"ensembl_gene_id"],type="ensembl_gene_id",seqType="3utr",mart=hmart)
+ print(seq)
+ }
Error in getBM(c(seqType, type), filters = type, values = id, mart = mart,  : 
  Query ERROR: caught BioMart::Exception: non-BioMart die(): DBD::mysql::st execute failed: File './sequence_mart_54/hsapiens_genomic_sequence__dna_chunks__main.MYD' not found (Errcode: 27) at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/GenomicSequence/DNAAdaptor.pm line 209.

I have attached the script that triggers the error.
Can anyone help me understand the cause of such a message so that I can try and find a work-around ?

Thank you very much in advance.

e tutti i telefonini TIM!
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