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Old 04-27-2010, 12:28 AM   #4
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

You might want to try setting a DISPLAY environment variable (export DISPLAY=:0.0) even if you're running on a headless system. If you specify a filename when launching FastQC then no windows should open, but since the program uses some swing classes behind the scenes then java might be getting itself confused.

I'll try to replicate this on one of our servers and see if I can trigger the same problem.
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