is.broadpeak FALSE 
read A549-100nM-Dex-5h-p300-Rep2-ENCLB473RRB.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  264494 peaks
 264494 peaks are left after cleaning
 A549-100nM-Dex-5h-p300-Rep3-ENCLB283CWG.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  157837 peaks
 157837  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549-100nM-Dex-5h-p300-Rep2-vs-Rep3-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-5h-p300-Rep2-vs-Rep3-em.sav 
EM estimation for the following files
A549-100nM-Dex-5h-p300-Rep2-ENCLB473RRB.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
A549-100nM-Dex-5h-p300-Rep3-ENCLB283CWG.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
$p
[1] 0.4854148

$rho1
[1] 0.8608217

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-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] 7903.909

$x.mean2
[1] 18379.66

$y.mean1
[1] 8310.923

$y.mean2
[1] 17995.63

$x.sd1
[1] 5919.205

$x.sd2
[1] 5303.574

$y.sd1
[1] 6484.252

$y.sd2
[1] 5409.006