is.broadpeak FALSE 
read A549-100nM-Dex-2h-p300-Rep2-ENCLB562LAQ.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  228661 peaks
 228661 peaks are left after cleaning
 A549-100nM-Dex-2h-p300-Rep3-ENCLB378YOD.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  271518 peaks
 271518  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549-100nM-Dex-2h-p300-Rep2-vs-Rep3-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-2h-p300-Rep2-vs-Rep3-em.sav 
EM estimation for the following files
A549-100nM-Dex-2h-p300-Rep2-ENCLB562LAQ.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
A549-100nM-Dex-2h-p300-Rep3-ENCLB378YOD.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
$p
[1] 0.4686058

$rho1
[1] 0.7667975

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-2h-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] 8491.74

$x.mean2
[1] 18218.76

$y.mean1
[1] 8779.229

$y.mean2
[1] 17965.13

$x.sd1
[1] 6570.924

$x.sd2
[1] 5881.478

$y.sd1
[1] 6790.584

$y.sd2
[1] 6066.251