is.broadpeak TRUE 
read H3K27ac_mH2A1i_MT_Rep1-GSM1972405.mm10.36mers.MACS-2.1.0.p1e-2.broad_peaks.broadPeak :  63719 peaks
 63719 peaks are left after cleaning
 H3K27ac_mH2A1i_MT_Rep2-GSM1972406.mm10.36mers.MACS-2.1.0.p1e-2.broad_peaks.broadPeak :  51527 peaks
 51527  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-2.broad_peaks-uri.sav 
EM is done

EM is saved at: IDR-H3K27ac_mH2A1i_MT.MACS-2.1.0.p1e-2.broad_peaks-em.sav 
EM estimation for the following files
H3K27ac_mH2A1i_MT_Rep1-GSM1972405.mm10.36mers.MACS-2.1.0.p1e-2.broad_peaks.broadPeak
H3K27ac_mH2A1i_MT_Rep2-GSM1972406.mm10.36mers.MACS-2.1.0.p1e-2.broad_peaks.broadPeak
$p
[1] 0.4632289

$rho1
[1] 0.07703274

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-H3K27ac_mH2A1i_MT.MACS-2.1.0.p1e-2.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] 12033.57

$x.mean2
[1] 12257.08

$y.mean1
[1] 11668.38

$y.mean2
[1] 12572.43

$x.sd1
[1] 7613.266

$x.sd2
[1] 6453.906

$y.sd1
[1] 7533.132

$y.sd2
[1] 6507.336