is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read A549-EtOH-Sin3a.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.arrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 A549-EtOH-Sin3a.pooled.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.arrowPeak.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-Sin3a.pseudoReps-uri.sav 
EM is done

EM is saved at: IDR-A549-EtOH-Sin3a.pseudoReps-em.sav 
EM estimation for the following files
A549-EtOH-Sin3a.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.arrowPeak.top100K-p-value-sort
A549-EtOH-Sin3a.pooled.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.arrowPeak.top100K-p-value-sort
$p
[1] 0.5228572

$rho1
[1] 0.7267108

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-EtOH-Sin3a.pseudoReps-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] 13387.23

$x.mean2
[1] 22028.68

$y.mean1
[1] 13300.27

$y.mean2
[1] 22123.95

$x.sd1
[1] 9748.045

$x.sd2
[1] 8425.046

$y.sd1
[1] 9554.951

$y.sd2
[1] 8567.434