is.broadpeak FALSE 
read A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.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-GR-Rep1-GSM2095218-vs-Rep2-GSM2095219-uri.sav 
EM is done

EM is saved at: IDR-A549-Dex-GR-Rep1-GSM2095218-vs-Rep2-GSM2095219-em.sav 
EM estimation for the following files
A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.3672458

$rho1
[1] 0.5623893

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-Dex-GR-Rep1-GSM2095218-vs-Rep2-GSM2095219-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] 404.0892

$x.mean2
[1] 629.2136

$y.mean1
[1] 400.4502

$y.mean2
[1] 631.429

$x.sd1
[1] 343.0485

$x.sd2
[1] 261.0616

$y.sd1
[1] 316.012

$y.sd2
[1] 279.2682