is.broadpeak FALSE 
read A549_EtOH_B2-DNAse-GSM2060822.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_B2-DNAse-GSM2060822-vs-GSM2060823-uri.sav 
EM is done

EM is saved at: IDR-A549_EtOH_B2-DNAse-GSM2060822-vs-GSM2060823-em.sav 
EM estimation for the following files
A549_EtOH_B2-DNAse-GSM2060822.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] 0.6849849

$rho1
[1] 0.9104159

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549_EtOH_B2-DNAse-GSM2060822-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] 24112.22

$x.mean2
[1] 49139.75

$y.mean1
[1] 24155.12

$y.mean2
[1] 49046.58

$x.sd1
[1] 15853.39

$x.sd2
[1] 10381.99

$y.sd1
[1] 15827.21

$y.sd2
[1] 10688.19