is.broadpeak TRUE 
read H3K27ac_MT_Rep1-GSM1972401.mm10.36mers.MACS-2.1.0.p1e-1.broad_peaks.broadPeak.top100K-p-value-sort :  60045 peaks
 60045 peaks are left after cleaning
 H3K27ac_MT_Rep2-GSM1972402.mm10.36mers.MACS-2.1.0.p1e-1.broad_peaks.broadPeak.top100K-p-value-sort :  44386 peaks
 44386  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: IDR-H3K27ac_MT.MACS-2.1.0.p1e-1.broad_peaks.broadPeak-uri.sav 
EM is done

EM is saved at: IDR-H3K27ac_MT.MACS-2.1.0.p1e-1.broad_peaks.broadPeak-em.sav 
EM estimation for the following files
H3K27ac_MT_Rep1-GSM1972401.mm10.36mers.MACS-2.1.0.p1e-1.broad_peaks.broadPeak.top100K-p-value-sort
H3K27ac_MT_Rep2-GSM1972402.mm10.36mers.MACS-2.1.0.p1e-1.broad_peaks.broadPeak.top100K-p-value-sort
$p
[1] 0.4257017

$rho1
[1] 0.1204502

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-H3K27ac_MT.MACS-2.1.0.p1e-1.broad_peaks.broadPeak-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] 12219.45

$x.mean2
[1] 11988.7

$y.mean1
[1] 12129.41

$y.mean2
[1] 12055.52

$x.sd1
[1] 7272.438

$x.sd2
[1] 6748.598

$y.sd1
[1] 7143.509

$y.sd2
[1] 6851.524