bedtools 2.0 merge - "unable to open file or unable to determine types"

Question

[Zev.Kronenberg]

I have a sorted bedfile comprised of three columns: seqid, start, and end.

sort -k1,1 -k2,2n tmp2.bed > tmp3.bed

1    6589256    6589207
1    11627195    12127194
1    12616616    12116617
1    18283067    18273068
1    21826932    21926931
1    28787213    28788212
1    31195434    31195483
1    39374350    39364351
1    42307024    42357023
1    47379997    47374998

~/tools/bedtools2/bin/bedtools merge -i tmp3.bed

Error: unable to open file or unable to determine types for file tmp3.bed

Probably something silly, but I'm not seeing it.

EDIT:

The second column - start must be before the end coordinates. It would be nice if bedtools threw an informative error as the user sucks.

[PoGibas]

bedtools do throw such error messages:

Error: malformed BED entry at line 1. Start was greater than end. Exiting.

I got this message using your example (bedtools v2.19.1).

[Zev.Kronenberg]

That is weird because my version is above your version number and I didn't get that error.

bedtools v2.21.0-2-g6a92b11

[Aaronquinlan]

What version of bedtools? Are you sure it is tab-delimited (check with cat -t)?

Answer 1

[trutane]

Another thing that will cause bedtools merge to produce this error is if the bed file contains an uncommented column header line such as:

chrom   start   end
1       243651534       243651752
1       243663020       243668636
1       243663020       243663088
1       243663038       243663088

Commenting the header with a leading # will make bedtools happy again:

#chrom   start   end
1       243651534       243651752
1       243663020       243668636
1       243663020       243663088
1       243663038       243663088

The bed file spec doesn't explicitly state anything about the legality of header lines or their expected format (e.g. should be preceded with '#'). Since the columns are proscribed for bed format, a header is not really necessary but can be convenient. Glad that bedtools supports it -- just don't forget to comment it!

bedtools version: 2.22.1

Answer 2

[mgadrianam]

I get the same error messages:

How did you solved. Could you please help me. I appreciated your help

Sincerely,
Adriana

[Leandro Lima]

awk '{if ($2 > $3) print $1"\t"$3"\t"$2; else print $1"\t"$2"\t"$3}' old.bed > new.bed

[Medhat]

Thanks a lot

Answer 3

[Zev.Kronenberg]

Solved: Some of the ends are before the starts. Stupid mistake.