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Old 06-20-2010, 11:20 PM   #59
Location: Melbourne

Join Date: Jan 2010
Posts: 21

Originally Posted by simonandrews View Post
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.

Thanks for the quick reply Simon.

The command I'm using is:

java -Xmx250m -classpath /Tools/FastQC/ sequence.fastq
and the sequence.fastq file I'm running it on is 2.9Gb (~17million 75bp reads)
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