Question: bedtools intersect segmentation fault
gravatar for ambarishnag
2.3 years ago by
ambarishnag0 wrote:


I am trying to run a command:

bedtools intersect -wao -f 0.75 -a A.gtf -b B.gtf > output.bed

and I get segmentation fault.

The command runs fine without the -wao option.

There are apparently no memory issues. I am running the code on a linux cluster and running the free -m command shows that there is enough memory on the node.

I looked that the bedtools intersect documentation and it mentions that the -wao option is restricted by the -f option. Is that what causing the segmentation fault ?

Your help will be greatly appreciated.


genomics bedtools • 1.1k views
ADD COMMENTlink modified 2.3 years ago by RamRS26k • written 2.3 years ago by ambarishnag0

Please use the formatting bar (especially the code option) to make your post more readable. Thank you!

enter image description here

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by RamRS26k
gravatar for Hussain Ather
2.3 years ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 wrote:

Which version of bedrolls are you running? There were some reports of segmentation faults with -wao with version 2.25 and updating to 2.26 might help.

ADD COMMENTlink written 2.3 years ago by Hussain Ather940
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