Hi, I am trying to use the code given below but I am getting this error Error: disk I/O error I was wondering what might be going wrong.

getGenePositions= function(gene.names,ensembl.version="nov2020.archive.ensembl.org",species="human"){
      if (species=="human"){
          ensembl = biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl",
                                     host=ensembl.version)
          gene.positions <- biomaRt::getBM(attributes=c('ensembl_gene_id','hgnc_symbol','chromosome_name','start_position','end_position'),
                                           filters ='hgnc_symbol', values =gene.names, mart = ensembl)
      }
        else {
            ensembl = biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl",
                                       host=ensembl.version)
            gene.positions <- biomaRt::getBM(attributes=c('ensembl_gene_id','mgi_symbol','chromosome_name','start_position','end_position'),
                                             filters ='mgi_symbol', values =gene.names, mart = ensembl)
        }
        gene.positions=gene.positions[!duplicated(gene.positions[,2]),]
        gene.positions[which(gene.positions[,3]=="X"),3]=23
        gene.positions[which(gene.positions[,3]=="Y"),3]=24
        gene.positions[which(gene.positions[,3]=="MT"),3]=0
        gene.positions[which(nchar(gene.positions[,3])>2),3]=0
        gene.positions=gene.positions[order(as.numeric(gene.positions[,3]),decreasing=F),]
        return(gene.positions)
}
gene.pos=getGenePositions(genes)

Thanks!

It may genuinely be a disk I/O error, i.e., you have no more disk space, or your quota has been exceeded, or your TMPDIR is full. Can you inform us about the system on which you are running R?

You see, biomaRt caches results. If you try getBM(..., useCache = FALSE), does that work?

Kevin