Question: Problem While Running Bedops
0
gravatar for ancient_learner
5.7 years ago by
India
ancient_learner610 wrote:

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?

bed sam • 1.5k views
ADD COMMENTlink modified 5.7 years ago by Malachi Griffith17k • written 5.7 years ago by ancient_learner610
1

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.

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by Vikas Bansal2.3k

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

ADD REPLYlink written 5.7 years ago by ancient_learner610

Update your kernel :)

ADD REPLYlink written 5.7 years ago by Vikas Bansal2.3k

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

ADD REPLYlink written 5.7 years ago by ancient_learner610

You can download source code and compile it, if you have GNU GCC 4.7 or greater installed. Grab a copy of source via svn and see the included README for compilation notes: http://code.google.com/p/bedops/source/checkout

ADD REPLYlink written 5.7 years ago by Alex Reynolds27k

Thank you alex i would do that

ADD REPLYlink written 5.7 years ago by ancient_learner610
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