is.broadpeak FALSE 
read A549-100nM-Dex-0.5h-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-0.5h-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-0.5h-p300.pseudoReps-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-0.5h-p300.pseudoReps-em.sav 
EM estimation for the following files
A549-100nM-Dex-0.5h-p300.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.arrowPeak.top100K-p-value-sort
A549-100nM-Dex-0.5h-p300.pooled.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.arrowPeak.top100K-p-value-sort
$p
[1] 0.6077187

$rho1
[1] 0.8949127

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-0.5h-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] 5628.377

$x.mean2
[1] 10655.6

$y.mean1
[1] 5652.633

$y.mean2
[1] 10618.14

$x.sd1
[1] 4035.507

$x.sd2
[1] 2922.044

$y.sd1
[1] 4080.753

$y.sd2
[1] 2888.858