intersectBed error: ${0%/*}/bedtools intersect "$@"

[pvz...@umich.edu]

Hi,

I am encountering an error when running: intersectBed -wa -s -c -a file1.bed -b file2.bed > output.bed, 

/usr/local/bin/intersectBed: line 2: 23109 Killed                  ${0%/*}/bedtools intersect "$@"

I tried running multiple times with different input files (also sorted files), and kept getting the same error, but with a different number after line 2: _____. 

Strangely enough, yesterday when I ran the same thing it seemed to work fine. 

Can you help?

Petra

[Aaron Quinlan]

Hi Petra,

Could you try running the following command, as unlike the intersectBed bash script you are using, it will run the actual bedtools executable and therefore hopefully give you deeper insight into the source of the problem:

bedtools intersect -wa -s -c -a file1.bed -b file2.bed > output.bed

Best,

Aaron

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[anton...@gmail.com]

I am confronted with the very same problem. If I use "intersectBed" I get an error message like this:

intersectBed -wo -a 1kb.bed -b ENCFF000STO.bam
/usr/bin/intersectBed: line 2: 19766 Killed                  ${0%/*}/bedtools intersect "$@"

Following Aron's advice, I get an even more cryptic error message:

intersect -wo -a 1kb.bed -b ENCFF000STO.bam
Killed

I am using bedtools v2.25.0.

Anton

[anton...@gmail.com]

I was just wondering if anyone has info on this problem (bug?). I am still running into this problem with various input files. Right now I am using bedtools v2.26.0.

Anton

[Ryan Dale]

Any chance you are running this on a cluster? Some clusters show a "Killed" message like this when a job on an interactive node runs out of allocated memory. How does it work with smaller input files or more memory?

-ryan

[liaomi...@gmail.com]

Hi Petra,

Have you solved this problem? I also met this problem for over one week and have no idea to handle it. If you have overcome the problem, may you please provide some advice? Thanks!

Mingzhi

在 2015年12月18日星期五 UTC-8下午3:24:48，pvz...@umich.edu写道：