is.broadpeak FALSE 
read A549-100nM-Dex-6h-p300-Rep1-ENCLB707OYP.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  325876 peaks
 325876 peaks are left after cleaning
 A549-100nM-Dex-6h-p300-Rep3-ENCLB312DIN.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  398396 peaks
 398396  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549-100nM-Dex-6h-p300-Rep1-vs-Rep3-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-6h-p300-Rep1-vs-Rep3-em.sav 
EM estimation for the following files
A549-100nM-Dex-6h-p300-Rep1-ENCLB707OYP.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
A549-100nM-Dex-6h-p300-Rep3-ENCLB312DIN.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
$p
[1] 0.3168397

$rho1
[1] 0.8691717

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-6h-p300-Rep1-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] 14102.28

$x.mean2
[1] 34728.36

$y.mean1
[1] 15556.53

$y.mean2
[1] 34052.89

$x.sd1
[1] 12256.3

$x.sd2
[1] 13527.88

$y.sd1
[1] 14072.79

$y.sd2
[1] 13682.67