is.broadpeak FALSE 
read A549-100nM-Dex-12h-p300-Rep1-ENCLB863RVB.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  263588 peaks
 263588 peaks are left after cleaning
 A549-100nM-Dex-12h-p300-Rep3-ENCLB898PLS.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  200940 peaks
 200940  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549-100nM-Dex-12h-p300-Rep1-vs-Rep3-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-12h-p300-Rep1-vs-Rep3-em.sav 
EM estimation for the following files
A549-100nM-Dex-12h-p300-Rep1-ENCLB863RVB.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
A549-100nM-Dex-12h-p300-Rep3-ENCLB898PLS.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
$p
[1] 0.4479437

$rho1
[1] 0.8662271

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-12h-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] 6070.733

$x.mean2
[1] 14915.61

$y.mean1
[1] 6530.004

$y.mean2
[1] 14542.6

$x.sd1
[1] 4616.554

$x.sd2
[1] 4478.539

$y.sd1
[1] 5163.408

$y.sd2
[1] 4690.591