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Old 06-20-2010, 11:07 PM   #57
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

Originally Posted by mard View Post
Processing sequence.fastq
Approx 5% complete for sequence.fastq
Exception in thread "AWT-AppKit" Exception in thread "Thread-3" java.lang.OutOfMemoryError: Java heap space
The error is because the program ran out of memory. The new version will use a bit more memory than the previous version since it looks at more sequences for the overrepresented sequence module. I've tested it with up to four 20million+ files open at the same time though and it was OK.

Can you let me know the exact command you are using to launch the program. If you're using the full java command you need to ensure that you add the -Xmx250m option to allocate a larger than default memory block to the program. If you use the fastqc wrapper then this should be added automatically.
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