is.broadpeak FALSE 
[1] "Fix 2 stops\n"
read SPP-300K-HepG2-CTCF-Broad-Rep1/HepG2-CTCF-Rep1-Broad.hg20-male.36mers.unique_VS_HepG2-Control-Rep1-Broad.hg20-male.36mers.unique.regionPeak :  60029 peaks
 60029 peaks are left after cleaning
 SPP-300K-HepG2-CTCF-Broad-Rep2/HepG2-CTCF-Rep2-Broad.hg20-male.36mers.unique_VS_HepG2-Control-Rep2-Broad.hg20-male.36mers.unique.regionPeak :  300000 peaks
 300000  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-HepG2-CTCF-Broad-uri.sav 
EM is done

EM is saved at: IDR-SPP-HepG2-CTCF-Broad-em.sav 
EM estimation for the following files
SPP-300K-HepG2-CTCF-Broad-Rep1/HepG2-CTCF-Rep1-Broad.hg20-male.36mers.unique_VS_HepG2-Control-Rep1-Broad.hg20-male.36mers.unique.regionPeak
SPP-300K-HepG2-CTCF-Broad-Rep2/HepG2-CTCF-Rep2-Broad.hg20-male.36mers.unique_VS_HepG2-Control-Rep2-Broad.hg20-male.36mers.unique.regionPeak
$p
[1] 0.8135791

$rho1
[1] 0.7822102

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-HepG2-CTCF-Broad-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] 21638.05

$x.mean2
[1] 41007.93

$y.mean1
[1] 22112.35

$y.mean2
[1] 38946.41

$x.sd1
[1] 13371.35

$x.sd2
[1] 7398.309

$y.sd1
[1] 13798.83

$y.sd2
[1] 8881.863