is.broadpeak FALSE 
read G1E-ER4-H3K27ac-538.mm10.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 G1E-ER4-H3K27ac-539.mm10.36mers.unique.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-G1E-ER4-H3K27ac-538-vs-539-uri.sav 
EM is done

EM is saved at: IDR-G1E-ER4-H3K27ac-538-vs-539-em.sav 
EM estimation for the following files
G1E-ER4-H3K27ac-538.mm10.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
G1E-ER4-H3K27ac-539.mm10.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.5802835

$rho1
[1] 0.926998

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-G1E-ER4-H3K27ac-538-vs-539-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] 18513.89

$x.mean2
[1] 40308.28

$y.mean1
[1] 18467.26

$y.mean2
[1] 40372.71

$x.sd1
[1] 13165.24

$x.sd2
[1] 9608.733

$y.sd1
[1] 13018.31

$y.sd2
[1] 9737.974