is.broadpeak FALSE 
read A549-100nM-Dex-3h-DNAse.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 A549-100nM-Dex-3h-DNAse.pooled.sorted.pseudoRep2.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-A549-100nM-Dex-3h-DNAse.pooled.sorted.pseudoRep-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-3h-DNAse.pooled.sorted.pseudoRep-em.sav 
EM estimation for the following files
A549-100nM-Dex-3h-DNAse.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
A549-100nM-Dex-3h-DNAse.pooled.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.7047947

$rho1
[1] 0.959902

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-3h-DNAse.pooled.sorted.pseudoRep-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] 27973.97

$x.mean2
[1] 59169.08

$y.mean1
[1] 27999.11

$y.mean2
[1] 59109.13

$x.sd1
[1] 17969.92

$x.sd2
[1] 10215.99

$y.sd1
[1] 18011.42

$y.sd2
[1] 10224.54