is.broadpeak FALSE 
[1] "Fix 6 stops\n"
[1] "Fix 3 stops\n"
read SPP-300K-K562-JunD-IggRabbit-SYDH-Rep1/K562-JunD-IggRabbit-Rep1-SYDH.hg20-female.36mers.unique_VS_K562-IggRabbit-SYDH.hg20-female.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-K562-JunD-IggRabbit-SYDH-Rep2/K562-JunD-IggRabbit-Rep2-SYDH.hg20-female.36mers.unique_VS_K562-IggRabbit-SYDH.hg20-female.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-K562-JunD-IggRabbit-SYDH-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-JunD-IggRabbit-SYDH-em.sav 
EM estimation for the following files
SPP-300K-K562-JunD-IggRabbit-SYDH-Rep1/K562-JunD-IggRabbit-Rep1-SYDH.hg20-female.36mers.unique_VS_K562-IggRabbit-SYDH.hg20-female.36mers.unique.regionPeak
SPP-300K-K562-JunD-IggRabbit-SYDH-Rep2/K562-JunD-IggRabbit-Rep2-SYDH.hg20-female.36mers.unique_VS_K562-IggRabbit-SYDH.hg20-female.36mers.unique.regionPeak
$p
[1] 0.5150737

$rho1
[1] 0.8885869

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-JunD-IggRabbit-SYDH-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] 40316.59

$x.mean2
[1] 83462.09

$y.mean1
[1] 41712.7

$y.mean2
[1] 81979.27

$x.sd1
[1] 30462.58

$x.sd2
[1] 25150.63

$y.sd1
[1] 30923.88

$y.sd2
[1] 26947.42