is.broadpeak FALSE 
read HepG2-DNAse-Rep1-UW.hg20-male.28mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 HepG2-DNAse-Rep2-UW.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: HepG2-DNAse-UW-Rep1-vs-Rep2-uri.sav 
EM is done

EM is saved at: HepG2-DNAse-UW-Rep1-vs-Rep2-em.sav 
EM estimation for the following files
HepG2-DNAse-Rep1-UW.hg20-male.28mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
HepG2-DNAse-Rep2-UW.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.6424229

$rho1
[1] 0.9153232

$rho2
[1] 0

Write overlapped peaks and local idr to: HepG2-DNAse-UW-Rep1-vs-Rep2-overlapped-peaks.txt
Write number of peaks above IDR cutoff [0.01, 0.25]: npeaks-aboveIDR.txt
Marginal mean of two components:
$x.mean1
[1] 17890.62

$x.mean2
[1] 35041.65

$y.mean1
[1] 17542.09

$y.mean2
[1] 35667.03

$x.sd1
[1] 12319.53

$x.sd2
[1] 8740.182

$y.sd1
[1] 12063.61

$y.sd2
[1] 8094.859