Hi Peter,

it runs on a single server since this Galaxy instance is for internal use of our lab only.

Aborting other long running tools like tophat and bowtie works just as expected. I have also noticed that at least a couple of times not only the cufflinks process(es) were not terminated but also that one of the Galaxy handler processes (five of them in our instance) crashed. I suspect that the two things are related but have no proof for that.


Il 18/02/14 15:24, Peter Cock ha scritto:
On Tue, Feb 18, 2014 at 2:20 PM, Federico Zambelli
<federico.zambe...@unimi.it> wrote:

something strange happens with Cufflinks in our Galaxy server. When a user
deletes a running Cufflinks job in fact the associated Cufflinks process(es)
are not terminated. Apart from unneccessary CPU usage, this prevents other
jobs from starting if the max jobs limit has been already reached by the

This happens only with Cufflinks, Cuffcompare for comparison behaves just


What cluster system are you using? Can you try a few other long
running tools for comparison?

I've been meaning to double check if this still happens, but I had seen
this for BLAST+ jobs under SGE (noticeable again when large zombie
jobs are blocking the queue).


Federico Zambelli, Ph.D.
Bioinformatics, Evolution and Comparative Genomics Lab
Dept. of Biosciences
University of Milano - Italy

What can be asserted without proof can be dismissed without proof.
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