is.broadpeak FALSE 
read A549_EtOH_B1-DNAse-GSM2060821.hg20-male.20mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 A549_EtOH_B3-DNAse-GSM2060823.hg20-male.20mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549_EtOH_B1-DNAse-GSM2060821-vs-GSM2060823-uri.sav 
EM is done

EM is saved at: IDR-A549_EtOH_B1-DNAse-GSM2060821-vs-GSM2060823-em.sav 
EM estimation for the following files
A549_EtOH_B1-DNAse-GSM2060821.hg20-male.20mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
A549_EtOH_B3-DNAse-GSM2060823.hg20-male.20mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.6596407

$rho1
[1] 0.9101298

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549_EtOH_B1-DNAse-GSM2060821-vs-GSM2060823-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] 22992.35

$x.mean2
[1] 47740.83

$y.mean1
[1] 23359.67

$y.mean2
[1] 47029.74

$x.sd1
[1] 15333.76

$x.sd2
[1] 10338.65

$y.sd1
[1] 15621.65

$y.sd2
[1] 11138.47