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_ensem bl",host="www.ensembl.org") Checking attributes ... ok Checking filters ... ok > gene.map <- getBM (attributes=c("hgnc_symbol","ensembl_gene_id","ens embl_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! [[alternative HTML version deleted]]