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Old 03-07-2014, 11:35 AM   #10
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
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Thanks for the recommendations, especially the ambig= one. The help for bbmap.sh is ... confusing, at least at first glance.

One thing I think is working but giving me an improper warning message is the -Xmx parameter. From starting like so:

Quote:
bbmap.sh -Xmx30G path=../BBMap_ref in1=$R1 in2=$R2 ...
I get:

Quote:
This system does not have ulimit set, so max memory cannot be determined. Attempting to use 4G.
If this fails, please set ulimit or run this program qsubbed or from a qlogin session on Genepool.
java -ea -Xmx30G ....
In other words a warning but Java itself is starting up properly with 30G.
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