Question: bedtools intersect segmentation fault
gravatar for ambarishnag
16 months 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 • 762 views
ADD COMMENTlink modified 16 months ago by RamRS21k • written 16 months ago by ambarishnag0

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

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ADD REPLYlink modified 16 months ago • written 16 months ago by RamRS21k
gravatar for Hussain Ather
16 months ago by
Hussain Ather910
National Institutes of Health, Bethesda, MD
Hussain Ather910 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 16 months ago by Hussain Ather910
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