is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1/G1E-ER4-24h-GATA1-Control-Rep1-ENCFF001MRX.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.regionPeak :  87738 peaks
 87738 peaks are left after cleaning
 SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2/G1E-ER4-24h-GATA1-Control-Rep2-ENCFF001MSL.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.30M.regionPeak :  300000 peaks
 300000  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-uri.sav 
EM is done

EM is saved at: IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-em.sav 
EM estimation for the following files
SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1/G1E-ER4-24h-GATA1-Control-Rep1-ENCFF001MRX.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.regionPeak
SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2/G1E-ER4-24h-GATA1-Control-Rep2-ENCFF001MSL.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.30M.regionPeak
$p
[1] 0.4036108

$rho1
[1] 0.8545714

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-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] 7064.092

$x.mean2
[1] 16244.23

$y.mean1
[1] 7296.734

$y.mean2
[1] 16086.54

$x.sd1
[1] 5634.996

$x.sd2
[1] 5682.307

$y.sd1
[1] 6226.886

$y.sd2
[1] 5510.293