is.broadpeak FALSE 
read K562-CTCF-Rep1-Broad.hg20-female.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 K562-CTCF-Rep2-Broad.hg20-female.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-K562-CTCF-Broad-Rep1-vs-Rep2-uri.sav 
EM is done

EM is saved at: IDR-K562-CTCF-Broad-Rep1-vs-Rep2-em.sav 
EM estimation for the following files
K562-CTCF-Rep1-Broad.hg20-female.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
K562-CTCF-Rep2-Broad.hg20-female.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.724086

$rho1
[1] 0.912458

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-K562-CTCF-Broad-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] 24055.5

$x.mean2
[1] 51127.01

$y.mean1
[1] 24239.73

$y.mean2
[1] 50644.38

$x.sd1
[1] 15171.66

$x.sd2
[1] 8127.115

$y.sd1
[1] 15311.69

$y.sd2
[1] 8982.024