is.broadpeak FALSE 
read A549-100nM-Dex-0.5h-p300-Rep2-ENCLB591AUL.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  241199 peaks
 241199 peaks are left after cleaning
 A549-100nM-Dex-0.5h-p300-Rep3-ENCLB923NAK.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  197609 peaks
 197609  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549-100nM-Dex-0.5h-p300-Rep2-vs-Rep3-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-0.5h-p300-Rep2-vs-Rep3-em.sav 
EM estimation for the following files
A549-100nM-Dex-0.5h-p300-Rep2-ENCLB591AUL.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
A549-100nM-Dex-0.5h-p300-Rep3-ENCLB923NAK.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
$p
[1] 0.3762676

$rho1
[1] 0.8318321

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-0.5h-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] 7396.304

$x.mean2
[1] 18052.94

$y.mean1
[1] 8300.041

$y.mean2
[1] 17506.73

$x.sd1
[1] 6179.749

$x.sd2
[1] 6285.437

$y.sd1
[1] 7144.04

$y.sd2
[1] 6526.177