cuffdiff was killed without any information?

Question

[i19870503]

I have 29 samples to run cuffdiff, before cuffdiff it runs smoothly. But I run cuffdiff several hours it shows that:

[17:23:59] Loading reference annotation and sequence.
Warning: No conditions are replicated, switching to 'blind' dispersion method
[17:24:41] Inspecting maps and determining fragment length distributions.
Killed

How can fix it?

Answer 1

[User 59]

Either the system, or an administrator of the system has killed the job. You probably ran out of memory.

[i19870503]

You are right, it runs without any error when I try to use less samples run the command.

So do you have any idea to limit the memory usage of cuffdiff?

[User 59]

See advice here: http://www.nature.com/nprot/journal/v7/n3/fig_tab/nprot.2012.016_T2.html