is.broadpeak FALSE 
[1] "Fix 4 stops\n"
[1] "Fix 1 stops\n"
read SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1/G1E-ER4-CTCF-Rep1-PSU.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2/G1E-ER4-CTCF-Rep2-PSU.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.regionPeak :  255016 peaks
 255016  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-uri.sav 
EM is done

EM is saved at: IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-em.sav 
EM estimation for the following files
SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1/G1E-ER4-CTCF-Rep1-PSU.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.regionPeak
SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2/G1E-ER4-CTCF-Rep2-PSU.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.regionPeak
$p
[1] 0.5501894

$rho1
[1] 0.8886221

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-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] 18002.12

$x.mean2
[1] 43852.33

$y.mean1
[1] 18062.03

$y.mean2
[1] 43779.07

$x.sd1
[1] 12319.27

$x.sd2
[1] 9858.369

$y.sd1
[1] 12271.06

$y.sd2
[1] 10120.02