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Old 03-26-2013, 10:55 AM   #9
Simon Anders
Senior Member
Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994

Well, maybe it is counting. The counts are written out only at the very end, and given that your SAM file is quite large, this might take quite a while. As you have switched off progress reports ("-q") you cannot say whether it is getting somewhere.
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