command error in intersectBed

[cmccabe]

I get the follwing error using this command: The bed files are attached. Thank you .

 ./intersectBed -a panel_merge.bed -b IDT.bed > intersectedIDT.bed

Please use tab-delimited BED, GFF, or VCF. Perhaps you have non-integer starts or ends at line 1?

[blancha]

Works perfectly for me, with the exact same files and command line, on CentOS 6 server with bedtools v2.20.0.

[cmccabe]

I am using ubuntu 12.0.4 and bedtools 2.17.0. Thanks

[blancha]

Just upgrade to the most recent version of bed tools.

I get the same error message as you with bedtools 2.17.0, whereas it works perfectly with bedtools 2.20.0, using exactly the same files and command line.

It's always best to start by updating to the latest software when faced with a mysterious bug.

[cmccabe]

Do I need to re-install the zlib, zlib-dev through sudo get-apt?

Do you know the commands I should use? Thanks

 sudo get-apt install bedtools 2.20.0

[blancha]

The best is to get the very latest version from GitHub.

https://github.com/arq5x/bedtools2/releases

Download the latest version.
Uncompress the file. Just type 'tar -xf *.tar' or tar -xzvf *.tar.gz' if the file is gzipped.
Change to the newly created bedtools folder.
Compile the code. Just type 'make'.
Done.

The binary files will be in the bin folder. Type the full path to the bin folder, or add the bin folder to your PATH environment variable to avoid having to type the full path each time.