is.broadpeak FALSE 
read 10Thalf-exp-H3K27ac-F3_5907092339-18002.mm10.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 10Thalf-exp-H3K27ac-G3_5907092340-18004.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: IDR-10Thalf-exp-H3K27ac-FR-vs-G3-uri.sav 
EM is done

EM is saved at: IDR-10Thalf-exp-H3K27ac-FR-vs-G3-em.sav 
EM estimation for the following files
10Thalf-exp-H3K27ac-F3_5907092339-18002.mm10.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
10Thalf-exp-H3K27ac-G3_5907092340-18004.mm10.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.6662487

$rho1
[1] 0.9199133

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-10Thalf-exp-H3K27ac-FR-vs-G3-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] 19010.93

$x.mean2
[1] 40675.96

$y.mean1
[1] 19039.08

$y.mean2
[1] 40619.86

$x.sd1
[1] 12537.54

$x.sd2
[1] 7831.518

$y.sd1
[1] 12533.28

$y.sd2
[1] 7998.239