Problem While Running Bedops

Question

[ancient_learner]

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?

[Vikas Bansal]

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.

[ancient_learner]

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

[Vikas Bansal]

Update your kernel :)

[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

[Alex Reynolds]

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

[ancient_learner]

Thank you alex i would do that