Question: cuffdiff was killed without any information?
0
gravatar for i19870503
4.0 years ago by
i1987050310
Australia
i1987050310 wrote:

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?

 

rna-seq • 1.7k views
ADD COMMENTlink modified 4.0 years ago by Daniel Swan13k • written 4.0 years ago by i1987050310
0
gravatar for Daniel Swan
4.0 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

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

ADD COMMENTlink written 4.0 years ago by Daniel Swan13k

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

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

ADD REPLYlink written 4.0 years ago by i1987050310

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

ADD REPLYlink written 4.0 years ago by Daniel Swan13k
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