is.broadpeak FALSE 
read SPP-300K-K562-CTCF-V0416101-HA-Rep1/K562-CTCF-V0416101-Rep1-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V0416101-Rep1-HA.hg20-female.36mers.unique.regionPeak :  77327 peaks
 77327 peaks are left after cleaning
 SPP-300K-K562-CTCF-V0416101-HA-Rep2/K562-CTCF-V0416101-Rep2-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V0416101-Rep2-HA.hg20-female.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-K562-CTCF-V0416101-HA-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-CTCF-V0416101-HA-em.sav 
EM estimation for the following files
SPP-300K-K562-CTCF-V0416101-HA-Rep1/K562-CTCF-V0416101-Rep1-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V0416101-Rep1-HA.hg20-female.36mers.unique.regionPeak
SPP-300K-K562-CTCF-V0416101-HA-Rep2/K562-CTCF-V0416101-Rep2-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V0416101-Rep2-HA.hg20-female.36mers.unique.regionPeak
$p
[1] 0.5281256

$rho1
[1] 0.8300208

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-CTCF-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] 9345.541

$x.mean2
[1] 18604.41

$y.mean1
[1] 9581.035

$y.mean2
[1] 18340.95

$x.sd1
[1] 6861.845

$x.sd2
[1] 5905.614

$y.sd1
[1] 6901.625

$y.sd2
[1] 6245.874