is.broadpeak FALSE 
read A549_Dex-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_Dex-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_Dex-DNAse.pooled.sorted.pseudoRep-uri.sav 
EM is done

EM is saved at: IDR-A549_Dex-DNAse.pooled.sorted.pseudoRep-em.sav 
EM estimation for the following files
A549_Dex-DNAse.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
A549_Dex-DNAse.pooled.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.6886273

$rho1
[1] 0.9615107

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549_Dex-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] 27126.54

$x.mean2
[1] 56292.19

$y.mean1
[1] 27045.39

$y.mean2
[1] 56471.43

$x.sd1
[1] 17855.85

$x.sd2
[1] 10612.14

$y.sd1
[1] 17761.07

$y.sd2
[1] 10467.67