is.broadpeak FALSE 
read A549-100nM-Dex-5h-p300-Rep1-ENCLB408ZKM.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  506228 peaks
 506228 peaks are left after cleaning
 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 cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549-100nM-Dex-5h-p300-Rep1-vs-Rep2-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-5h-p300-Rep1-vs-Rep2-em.sav 
EM estimation for the following files
A549-100nM-Dex-5h-p300-Rep1-ENCLB408ZKM.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
A549-100nM-Dex-5h-p300-Rep2-ENCLB473RRB.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
$p
[1] 0.3472351

$rho1
[1] 0.8397495

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-5h-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] 11343.07

$x.mean2
[1] 26504.55

$y.mean1
[1] 10744.25

$y.mean2
[1] 26823.59

$x.sd1
[1] 9752.249

$x.sd2
[1] 9986.869

$y.sd1
[1] 9328.518

$y.sd2
[1] 9699.385