is.broadpeak FALSE 
read SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1/A549-100nM-Dex-1h-CTCF-Rep1-HA.hg20.36mers.unique_VS_A549-100nM-Dex-1h-1PCR_Input-Rep1-HA.hg20.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2/A549-100nM-Dex-1h-CTCF-Rep2-HA.hg20.36mers.unique_VS_A549-100nM-Dex-1h-1PCR_Input-Rep1_V0422111-HA.hg20.36mers.unique.regionPeak :  154827 peaks
 154827  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-uri.sav 
EM is done

EM is saved at: IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-em.sav 
EM estimation for the following files
SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1/A549-100nM-Dex-1h-CTCF-Rep1-HA.hg20.36mers.unique_VS_A549-100nM-Dex-1h-1PCR_Input-Rep1-HA.hg20.36mers.unique.regionPeak
SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2/A549-100nM-Dex-1h-CTCF-Rep2-HA.hg20.36mers.unique_VS_A549-100nM-Dex-1h-1PCR_Input-Rep1_V0422111-HA.hg20.36mers.unique.regionPeak
$p
[1] 0.6978289

$rho1
[1] 0.9056529

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-A549-100nM-Dex-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] 18632.57

$x.mean2
[1] 39875.71

$y.mean1
[1] 18490.36

$y.mean2
[1] 40203.51

$x.sd1
[1] 11786.22

$x.sd2
[1] 7530.542

$y.sd1
[1] 11705.6

$y.sd2
[1] 6855.175