is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read 10Thalf-exp-H3K27ac-18002-vs-18004.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 10Thalf-exp-H3K27ac-18002-vs-18004.pooled.sorted.pseudoRep2.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-18002-vs-18004.pooled.sorted.pseudoRep-uri.sav 
EM is done

EM is saved at: IDR-10Thalf-exp-H3K27ac-18002-vs-18004.pooled.sorted.pseudoRep-em.sav 
EM estimation for the following files
10Thalf-exp-H3K27ac-18002-vs-18004.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
10Thalf-exp-H3K27ac-18002-vs-18004.pooled.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.6596992

$rho1
[1] 0.9465128

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-10Thalf-exp-H3K27ac-18002-vs-18004.pooled.sorted.pseudoRep-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] 20961.25

$x.mean2
[1] 44990.5

$y.mean1
[1] 21035.5

$y.mean2
[1] 44846.76

$x.sd1
[1] 13943.92

$x.sd2
[1] 8595.896

$y.sd1
[1] 14067.04

$y.sd2
[1] 8607.499