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Old 10-23-2013, 07:01 PM   #4
Kennels
Senior Member
 
Location: Sydney

Join Date: Feb 2011
Posts: 149
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Try also putting '-q' option to specify it is fastq input.
If that still fails, what is the output from

Code:
head NA11881.fastq
some check questions:

Can you post any errors or warning you are getting?
Do you have all the index files in the same directory?
Do you have 8 cpus on your computer?
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