is.broadpeak FALSE 
read A549-100nM-Dex-0h-p300-Rep1-ENCLB241KYA.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  317768 peaks
 317768 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-Rep1-vs-Rep3-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-0h-p300-Rep1-vs-Rep3-em.sav 
EM estimation for the following files
A549-100nM-Dex-0h-p300-Rep1-ENCLB241KYA.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] 0.3224967

$rho1
[1] 0.6170883

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-0h-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] 12184.56

$x.mean2
[1] 17181.26

$y.mean1
[1] 8918.37

$y.mean2
[1] 18740.04

$x.sd1
[1] 9958.61

$x.sd2
[1] 7993.558

$y.sd1
[1] 6843.878

$y.sd2
[1] 8110.193