is.broadpeak FALSE 
read A549-100nM-Dex-2h-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-2h-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-2h-DNAse.pooled.sorted.pseudoRep-uri.sav 
EM is done

EM is saved at: IDR-A549-100nM-Dex-2h-DNAse.pooled.sorted.pseudoRep-em.sav 
EM estimation for the following files
A549-100nM-Dex-2h-DNAse.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
A549-100nM-Dex-2h-DNAse.pooled.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.6997353

$rho1
[1] 0.9569416

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-A549-100nM-Dex-2h-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] 27797.55

$x.mean2
[1] 58800.59

$y.mean1
[1] 27797.93

$y.mean2
[1] 58799.7

$x.sd1
[1] 17941.37

$x.sd2
[1] 10289.31

$y.sd1
[1] 17913.18

$y.sd2
[1] 10405.64