is.broadpeak FALSE 
[1] "Fix 10 stops\n"
[1] "Fix 5 stops\n"
read SPP-300K-K562-MAX-IggRabbit-SYDH-Rep1/K562-MAX-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-MAX-IggRabbit-SYDH-Rep2/K562-MAX-IggRabbit-Rep2-SYDH.hg20-female.36mers.unique_VS_K562-IggRabbit-SYDH.hg20-female.36mers.unique.regionPeak :  219113 peaks
 219113  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-K562-MAX-IggRabbit-SYDH-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-MAX-IggRabbit-SYDH-em.sav 
EM estimation for the following files
SPP-300K-K562-MAX-IggRabbit-SYDH-Rep1/K562-MAX-IggRabbit-Rep1-SYDH.hg20-female.36mers.unique_VS_K562-IggRabbit-SYDH.hg20-female.36mers.unique.regionPeak
SPP-300K-K562-MAX-IggRabbit-SYDH-Rep2/K562-MAX-IggRabbit-Rep2-SYDH.hg20-female.36mers.unique_VS_K562-IggRabbit-SYDH.hg20-female.36mers.unique.regionPeak
$p
[1] 0.5165442

$rho1
[1] 0.8758273

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-MAX-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] 31992.08

$x.mean2
[1] 60613.94

$y.mean1
[1] 30255.07

$y.mean2
[1] 62469.69

$x.sd1
[1] 23933.36

$x.sd2
[1] 20310.96

$y.sd1
[1] 22523.44

$y.sd2
[1] 19225.4