Have you ensured that you're always using tabs to separate the columns? I've seen a couple files with spaces randomly thrown in and that tends to break things.

Try: perl -p -i -e 's/ /\t/g' bed_file.txt for converting white spaces to tabs and rerun bedtools.

As others have suggested, this is most likely caused by the file having spaces in place of tabs. I note you mention this table was written in R, where the default separator for write.table is indeed a space. I have this function in my .Rprofile to make writing bioinformatic-sy table easier:

write.simple.table <- function(...){
    write.table(..., quote=FALSE, row.names=FALSE, col.names=FALSE, sep='\t')
}

Error: unable to open file or unable to determine types for file

Hi i am trying to run this commands bedtools intersect -a Ec_k12.gff -b target_genes.txt -f 0.5 -wa -wb > genes_with_coordinates.bed and i am getting this error even after following given steps regarding this error on biostars/google. please help me if anyone know how to solve it? and the error is -

Error: unable to open file or unable to determine types for file / target_genes.tx

- Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in the
  expected columns (e.g., cols 2 and 3 for BED).

thank you !