is.broadpeak FALSE 
read A549-100nM-Dex-2h-p300-Rep1-ENCLB897VWI.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  337910 peaks
 337910 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-Rep1-vs-Rep3-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-2h-p300-Rep1-vs-Rep3-em.sav 
EM estimation for the following files
A549-100nM-Dex-2h-p300-Rep1-ENCLB897VWI.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] 0.3351722

$rho1
[1] 0.7707324

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-2h-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] 9371.78

$x.mean2
[1] 15619.3

$y.mean1
[1] 7870.637

$y.mean2
[1] 16378.16

$x.sd1
[1] 7942.796

$x.sd2
[1] 6835.677

$y.sd1
[1] 6808.479

$y.sd2
[1] 6632.356