is.broadpeak FALSE 
read HepG2-FOXA2-Rep1-HA.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 HepG2-FOXA2-Rep2-HA.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: IDR-HepG2-FOXA2-HA-Rep1-vs-Rep2-uri.sav 
EM is done

EM is saved at: IDR-HepG2-FOXA2-HA-Rep1-vs-Rep2-em.sav 
EM estimation for the following files
HepG2-FOXA2-Rep1-HA.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
HepG2-FOXA2-Rep2-HA.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.6336111

$rho1
[1] 0.6168581

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-HepG2-FOXA2-HA-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] 12368.7

$x.mean2
[1] 21811.77

$y.mean1
[1] 12523.18

$y.mean2
[1] 21545.12

$x.sd1
[1] 8794.694

$x.sd2
[1] 6143.805

$y.sd1
[1] 8412.465

$y.sd2
[1] 7350.076