is.broadpeak FALSE 
read G1E-ER4-DNAse-ENCFF001LUL-PSU.mm10.20mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 G1E-ER4-DNAse-ENCFF001LUS-PSU.mm10.20mers.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: G1E-ER4-DNAse-ENCFF001LUL-PSU-vs-Rep2-uri.sav 
EM is done

EM is saved at: G1E-ER4-DNAse-ENCFF001LUL-PSU-vs-Rep2-em.sav 
EM estimation for the following files
G1E-ER4-DNAse-ENCFF001LUL-PSU.mm10.20mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
G1E-ER4-DNAse-ENCFF001LUS-PSU.mm10.20mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.7336403

$rho1
[1] 0.6357492

$rho2
[1] 0

Write overlapped peaks and local idr to: G1E-ER4-DNAse-ENCFF001LUL-PSU-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] 13022.78

$x.mean2
[1] 23707.19

$y.mean1
[1] 13120.04

$y.mean2
[1] 23440.29

$x.sd1
[1] 8348.079

$x.sd2
[1] 6291.825

$y.sd1
[1] 8523.973

$y.sd2
[1] 6086.861