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Old 03-09-2015, 09:05 AM   #46
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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I think I see the problem - you're using the wrong file name for the reads:

bbduk.sh in=interleaved.gz out=trimmed.fq.gz ktrim=r k=23 hdist=1 mink=11 tpe tbo minlen=90 ref=truseq.fa.gz,nextera.fa.gz

bbmap.sh maxindex=200 in=trimmed.fq.fq mhist=mhist.txt bhist=bhist.txt qhist=qhist.txt qahist=qahist.txt

...

Reads Used: 0 (0 bases)

Normally, BBMap should throw an exception saying it can't find the input file if it does not exist, so I assume there is an empty file named "trimmed.fq.fq".
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