This is just a guess but you appear to have an extra "-" in the index option at the end of the command?
You can also try the repair.sh utility from BBmap suite that can achieve the same result: http://seqanswers.com/forums/showthr...t=41057&page=4
You can also try the repair.sh utility from BBmap suite that can achieve the same result: http://seqanswers.com/forums/showthr...t=41057&page=4
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