bedtools intersect segmentation fault

Question

[ambarishnag]

Hi,

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.

Thanks

[Ram]

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Answer 1

[Hussain Ather]

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.