is.broadpeak FALSE 
read SPP-300K-G1E-GATA2-ENCFF001MOI-vs-ENCFF001MOM-Rep1/G1E-GATA2-Rep1-ENCFF001MOI.mm10.36mers.unique_VS_G1E-Control-Rep1-ENCFF001MOR.mm10.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-G1E-GATA2-ENCFF001MOI-vs-ENCFF001MOM-Rep2/G1E-GATA2-Rep2-ENCFF001MOM.mm10.36mers.unique_VS_G1E-Control-Rep2-ENCFF001MPG.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-GATA2-ENCFF001MOI-vs-ENCFF001MOM-uri.sav 
EM is done

EM is saved at: IDR-SPP-G1E-GATA2-ENCFF001MOI-vs-ENCFF001MOM-em.sav 
EM estimation for the following files
SPP-300K-G1E-GATA2-ENCFF001MOI-vs-ENCFF001MOM-Rep1/G1E-GATA2-Rep1-ENCFF001MOI.mm10.36mers.unique_VS_G1E-Control-Rep1-ENCFF001MOR.mm10.36mers.unique.regionPeak
SPP-300K-G1E-GATA2-ENCFF001MOI-vs-ENCFF001MOM-Rep2/G1E-GATA2-Rep2-ENCFF001MOM.mm10.36mers.unique_VS_G1E-Control-Rep2-ENCFF001MPG.mm10.36mers.unique.regionPeak
$p
[1] 0.1150495

$rho1
[1] 0.6667295

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-G1E-GATA2-ENCFF001MOI-vs-ENCFF001MOM-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] 19432.9

$x.mean2
[1] 23494.14

$y.mean1
[1] 16270.82

$y.mean2
[1] 23908.6

$x.sd1
[1] 13768.17

$x.sd2
[1] 13154.22

$y.sd1
[1] 13278.95

$y.sd2
[1] 13035.3