is.broadpeak TRUE 
read H3K27ac_mH2A1i_MT_Rep1-GSM1972405.mm10.36mers.MACS-2.1.0.p1e-1.broad_peaks.broadPeak.top100K-p-value-sort :  63720 peaks
 63720 peaks are left after cleaning
 H3K27ac_mH2A1i_MT_Rep2-GSM1972406.mm10.36mers.MACS-2.1.0.p1e-1.broad_peaks.broadPeak.top100K-p-value-sort :  51533 peaks
 51533  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-H3K27ac_mH2A1i_MT.MACS-2.1.0.p1e-1.broad_peaks-uri.sav 
EM is done

EM is saved at: IDR-H3K27ac_mH2A1i_MT.MACS-2.1.0.p1e-1.broad_peaks-em.sav 
EM estimation for the following files
H3K27ac_mH2A1i_MT_Rep1-GSM1972405.mm10.36mers.MACS-2.1.0.p1e-1.broad_peaks.broadPeak.top100K-p-value-sort
H3K27ac_mH2A1i_MT_Rep2-GSM1972406.mm10.36mers.MACS-2.1.0.p1e-1.broad_peaks.broadPeak.top100K-p-value-sort
$p
[1] 0.4640327

$rho1
[1] 0.07655875

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-H3K27ac_mH2A1i_MT.MACS-2.1.0.p1e-1.broad_peaks-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] 12007.54

$x.mean2
[1] 12280.88

$y.mean1
[1] 11694.22

$y.mean2
[1] 12552.31

$x.sd1
[1] 7614.423

$x.sd2
[1] 6450.525

$y.sd1
[1] 7531.114

$y.sd2
[1] 6511.162