is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read A549-100nM-Dex-6h-p300-Rep2-ENCLB916AFA.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  539854 peaks
 539854 peaks are left after cleaning
 A549-100nM-Dex-6h-p300-Rep3-ENCLB312DIN.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  398396 peaks
 398396  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549-100nM-Dex-6h-p300-Rep2-vs-Rep3-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-6h-p300-Rep2-vs-Rep3-em.sav 
EM estimation for the following files
A549-100nM-Dex-6h-p300-Rep2-ENCLB916AFA.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
A549-100nM-Dex-6h-p300-Rep3-ENCLB312DIN.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
$p
[1] 0.3110601

$rho1
[1] 0.8308184

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-6h-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] 15807.55

$x.mean2
[1] 42144.07

$y.mean1
[1] 16554.19

$y.mean2
[1] 41806.52

$x.sd1
[1] 13668.24

$x.sd2
[1] 16035.11

$y.sd1
[1] 13785.11

$y.sd2
[1] 16525.38