is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read SPP-300K-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-Rep1/G1E-ER4-24h-GATA2-Rep1-ENCFF001MSD.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-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-Rep2/G1E-ER4-24h-GATA2-Rep2-ENCFF001MSI.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.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-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-uri.sav 
EM is done

EM is saved at: IDR-SPP-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-em.sav 
EM estimation for the following files
SPP-300K-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-Rep1/G1E-ER4-24h-GATA2-Rep1-ENCFF001MSD.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.regionPeak
SPP-300K-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-Rep2/G1E-ER4-24h-GATA2-Rep2-ENCFF001MSI.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.regionPeak
$p
[1] 0.1989181

$rho1
[1] 0.440662

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-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] 19509.27

$x.mean2
[1] 27079.26

$y.mean1
[1] 24054.8

$y.mean2
[1] 25946.38

$x.sd1
[1] 13695.31

$x.sd2
[1] 14627.84

$y.sd1
[1] 15787.13

$y.sd2
[1] 14467.97