is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read SPP-300K-HepG2-CTCF-HA-Rep1/HepG2-CTCF-Rep1-HA.hg20-male.36mers.unique_VS_HepG2-1PCR-Input-Rep1-HA.hg20-male.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-HepG2-CTCF-HA-Rep2/HepG2-CTCF-Rep2-HA.hg20-male.36mers.unique_VS_HepG2-1PCR-Input-Rep2-HA.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-HA-uri.sav 
EM is done

EM is saved at: IDR-SPP-HepG2-CTCF-HA-em.sav 
EM estimation for the following files
SPP-300K-HepG2-CTCF-HA-Rep1/HepG2-CTCF-Rep1-HA.hg20-male.36mers.unique_VS_HepG2-1PCR-Input-Rep1-HA.hg20-male.36mers.unique.regionPeak
SPP-300K-HepG2-CTCF-HA-Rep2/HepG2-CTCF-Rep2-HA.hg20-male.36mers.unique_VS_HepG2-1PCR-Input-Rep2-HA.hg20-male.36mers.unique.regionPeak
$p
[1] 0.7077069

$rho1
[1] 0.9267535

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-HepG2-CTCF-HA-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] 28612.48

$x.mean2
[1] 60714.75

$y.mean1
[1] 28201.1

$y.mean2
[1] 61709.48

$x.sd1
[1] 18103.98

$x.sd2
[1] 11112.84

$y.sd1
[1] 17737.93

$y.sd2
[1] 9484.448