is.broadpeak FALSE 
[1] "Fix 2 stops\n"
read A549-EtOH-Sin3a-Rep1-HA.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  582927 peaks
 582927 peaks are left after cleaning
 A549-EtOH-Sin3a-Rep2-HA.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak :  367228 peaks
 367228  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-A549-EtOH-Sin3a-Rep1-vs-Rep2-uri.sav 
EM is done

EM is saved at: IDR-A549-EtOH-Sin3a-Rep1-vs-Rep2-em.sav 
EM estimation for the following files
A549-EtOH-Sin3a-Rep1-HA.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
A549-EtOH-Sin3a-Rep2-HA.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak
$p
[1] 0.4036895

$rho1
[1] 0.6029698

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-EtOH-Sin3a-Rep1-vs-Rep2-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] 35774.15

$x.mean2
[1] 70999.66

$y.mean1
[1] 38664.62

$y.mean2
[1] 69042.19

$x.sd1
[1] 27067.21

$x.sd2
[1] 28362.58

$y.sd1
[1] 30481.82

$y.sd2
[1] 28280.27