is.broadpeak TRUE 
read H3K27ac_MT_Rep1-GSM1972401.mm10.36mers.MACS-2.1.0.p1e-2.broad_peaks.broadPeak :  60042 peaks
 60042 peaks are left after cleaning
 H3K27ac_MT_Rep2-GSM1972402.mm10.36mers.MACS-2.1.0.p1e-2.broad_peaks.broadPeak :  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-2.broad_peaks.broadPeak-uri.sav 
EM is done

EM is saved at: IDR-H3K27ac_MT.MACS-2.1.0.p1e-2.broad_peaks.broadPeak-em.sav 
EM estimation for the following files
H3K27ac_MT_Rep1-GSM1972401.mm10.36mers.MACS-2.1.0.p1e-2.broad_peaks.broadPeak
H3K27ac_MT_Rep2-GSM1972402.mm10.36mers.MACS-2.1.0.p1e-2.broad_peaks.broadPeak
$p
[1] 0.4258598

$rho1
[1] 0.1204251

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-H3K27ac_MT.MACS-2.1.0.p1e-2.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] 12228.94

$x.mean2
[1] 11981.59

$y.mean1
[1] 12131.34

$y.mean2
[1] 12054.08

$x.sd1
[1] 7273.779

$x.sd2
[1] 6747.124

$y.sd1
[1] 7143.843

$y.sd2
[1] 6851.168