is.broadpeak FALSE 
read A549-100nM-Dex-3h-p300-Rep1-ENCLB625GUO.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  244130 peaks
 244130 peaks are left after cleaning
 A549-100nM-Dex-3h-p300-Rep2-ENCLB793QJK.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  234323 peaks
 234323  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549-100nM-Dex-3h-p300-Rep1-vs-Rep2-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-3h-p300-Rep1-vs-Rep2-em.sav 
EM estimation for the following files
A549-100nM-Dex-3h-p300-Rep1-ENCLB625GUO.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
A549-100nM-Dex-3h-p300-Rep2-ENCLB793QJK.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
$p
[1] 0.457149

$rho1
[1] 0.848261

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-3h-p300-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] 6971.059

$x.mean2
[1] 15625.43

$y.mean1
[1] 6598.071

$y.mean2
[1] 15939.77

$x.sd1
[1] 5539.204

$x.sd2
[1] 4846.036

$y.sd1
[1] 4909.561

$y.sd2
[1] 4834.427