is.broadpeak FALSE 
read A549-100nM-Dex-12h-p300.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.arrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 A549-100nM-Dex-12h-p300.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-A549-100nM-Dex-12h-p300.pseudoReps-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-12h-p300.pseudoReps-em.sav 
EM estimation for the following files
A549-100nM-Dex-12h-p300.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.arrowPeak.top100K-p-value-sort
A549-100nM-Dex-12h-p300.pooled.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.arrowPeak.top100K-p-value-sort
$p
[1] 0.6093878

$rho1
[1] 0.9146501

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-12h-p300.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] 5936.496

$x.mean2
[1] 12305.75

$y.mean1
[1] 5980.451

$y.mean2
[1] 12237.36

$x.sd1
[1] 4076.178

$x.sd2
[1] 3156.099

$y.sd1
[1] 4136.952

$y.sd2
[1] 3169.831