is.broadpeak FALSE 
read SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1/A549-EtOH-1h-CTCF-Rep1-HA.hg20.36mers.unique_VS_A549-EtOH-1h-1PCR_Input-Rep1-HA.hg20.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2/A549-EtOH-1h-CTCF-Rep2-HA.hg20.36mers.unique_VS_A549-EtOH-1h-1PCR_Input-V0416101-HA.hg20.36mers.unique.regionPeak :  162678 peaks
 162678  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-uri.sav 
EM is done

EM is saved at: IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-em.sav 
EM estimation for the following files
SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1/A549-EtOH-1h-CTCF-Rep1-HA.hg20.36mers.unique_VS_A549-EtOH-1h-1PCR_Input-Rep1-HA.hg20.36mers.unique.regionPeak
SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2/A549-EtOH-1h-CTCF-Rep2-HA.hg20.36mers.unique_VS_A549-EtOH-1h-1PCR_Input-V0416101-HA.hg20.36mers.unique.regionPeak
$p
[1] 0.7496541

$rho1
[1] 0.922613

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-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] 20731.1

$x.mean2
[1] 42369.58

$y.mean1
[1] 20626.51

$y.mean2
[1] 42681.99

$x.sd1
[1] 12951.15

$x.sd2
[1] 7569.647

$y.sd1
[1] 12866.83

$y.sd2
[1] 7081.802