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Old 04-27-2010, 08:02 AM   #6
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871
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OK, it turns out there are two problems here.

One, as lletourn pointed out is that if you're running a headless server you need to add -Djava.awt.headless=true

There is also a change I need to make internally to FastQC to stop it trying to set up a graphical window (which it never displays) if it's running non-interactively.

I'll try to get an update out tomorrow with a fix for the internal problem and better instructions.
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