is.broadpeak FALSE 
[1] "Fix 3 stops\n"
[1] "Fix 1 stops\n"
read C2C12-myocyte-DNAse-Rep1.mm10.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 C2C12-myocyte-DNAse-Rep2.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: C2C12-myocyte-DNAse-Rep1-vs-Rep2-uri.sav 
EM is done

EM is saved at: C2C12-myocyte-DNAse-Rep1-vs-Rep2-em.sav 
EM estimation for the following files
C2C12-myocyte-DNAse-Rep1.mm10.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
C2C12-myocyte-DNAse-Rep2.mm10.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.7504496

$rho1
[1] 0.9816223

$rho2
[1] 0

Write overlapped peaks and local idr to: C2C12-myocyte-DNAse-Rep1-vs-Rep2-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] 35050.16

$x.mean2
[1] 73175.29

$y.mean1
[1] 35052.15

$y.mean2
[1] 73169.33

$x.sd1
[1] 21867.7

$x.sd2
[1] 11130.09

$y.sd1
[1] 21849.68

$y.sd2
[1] 11256.03