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Problem While Running Bedops

Hello I wanted to convert the .sam file to .bed format. I have used the following command in bedops to accomplish that

sam2bed sam2bed.foo.sam | sort-bed - > sorted-reads.bed

However i am getting the error like this

FATAL: kernel too old
Segmentation fault (core dumped)

The same happened with bedops-v2.0.0a as well as bedops-v2.2.0 versions. Do i have to install samtools to do this will it not be done by bedops alone?

sam bed
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updated by Malachi Griffith Malachi Griffith • written by ancient_learner ancient_learner

I think the error is because of the kernel version and may be bedops was not compiled to support older kernel versions (how old I don't know). But you can check your kernel version with command uname -r.

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written by Vikas Bansal Vikas Bansal

Probably that would be the reason so what can i do for this?

• 0 views • link
written by ancient_learner ancient_learner

Hmm i am doing it in common server and it is not in my hands to do so. however i have installed it using cygwin in the local system and seems to be fine thank you for your help

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written by ancient_learner ancient_learner

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