is.broadpeak FALSE 
[1] "Fix 8 stops\n"
read SPP-300K-K562-USF1-V0416101-HA-Rep1/K562-USF1-V0416101-Rep1-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V0416101-Rep1-HA.hg20-female.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-K562-USF1-V0416101-HA-Rep2/K562-USF1-V0416101-Rep2-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V0416101-Rep2-HA.hg20-female.36mers.unique.regionPeak :  95261 peaks
 95261  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-K562-USF1-V0416101-HA-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-USF1-V0416101-HA-em.sav 
EM estimation for the following files
SPP-300K-K562-USF1-V0416101-HA-Rep1/K562-USF1-V0416101-Rep1-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V0416101-Rep1-HA.hg20-female.36mers.unique.regionPeak
SPP-300K-K562-USF1-V0416101-HA-Rep2/K562-USF1-V0416101-Rep2-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V0416101-Rep2-HA.hg20-female.36mers.unique.regionPeak
$p
[1] 0.4550167

$rho1
[1] 0.9135866

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-USF1-V0416101-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] 14318.67

$x.mean2
[1] 29244.5

$y.mean1
[1] 13874.08

$y.mean2
[1] 29615.85

$x.sd1
[1] 11236.03

$x.sd2
[1] 10071.36

$y.sd1
[1] 11100.78

$y.sd2
[1] 9621.178