is.broadpeak FALSE 
read A549-100nM-Dex-0h-p300-Rep2-ENCLB768PAR.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  210226 peaks
 210226 peaks are left after cleaning
 A549-100nM-Dex-0h-p300-Rep3-ENCLB136AFU.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  390175 peaks
 390175  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549-100nM-Dex-0h-p300-Rep2-vs-Rep3-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-0h-p300-Rep2-vs-Rep3-em.sav 
EM estimation for the following files
A549-100nM-Dex-0h-p300-Rep2-ENCLB768PAR.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
A549-100nM-Dex-0h-p300-Rep3-ENCLB136AFU.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
$p
[1] 0.4880896

$rho1
[1] 0.5953948

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-0h-p300-Rep2-vs-Rep3-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] 8271.801

$x.mean2
[1] 16131.73

$y.mean1
[1] 8441.126

$y.mean2
[1] 15970.25

$x.sd1
[1] 6463.761

$x.sd2
[1] 5330.286

$y.sd1
[1] 5910.236

$y.sd2
[1] 6117.907