is.broadpeak FALSE 
read A549_Dex_B1-DNAse-GSM2060818.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_Dex_B3-DNAse-GSM2060820.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_Dex_B1-DNAse-GSM2060818-vs-GSM2060820-uri.sav 
EM is done

EM is saved at: IDR-A549_Dex_B1-DNAse-GSM2060818-vs-GSM2060820-em.sav 
EM estimation for the following files
A549_Dex_B1-DNAse-GSM2060818.hg20-male.20mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
A549_Dex_B3-DNAse-GSM2060820.hg20-male.20mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.659311

$rho1
[1] 0.9345655

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549_Dex_B1-DNAse-GSM2060818-vs-GSM2060820-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] 23806.36

$x.mean2
[1] 48810.08

$y.mean1
[1] 24148.78

$y.mean2
[1] 48148.13

$x.sd1
[1] 15986.63

$x.sd2
[1] 10750.26

$y.sd1
[1] 16251.7

$y.sd2
[1] 11466.75