is.broadpeak FALSE 
[1] "Fix 5 stops\n"
[1] "Fix 2 stops\n"
read SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1/C2C12-myocyte-MEF2-37C-5273-IP-F3-5272-16272.mm10.36mers.unique_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2/C2C12-60h-MEF2-B4-37oC-5404-5406-IP-3F-16504.mm10.36mers.unique_VS_C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.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-C2C12-60h-MEF2-37C-16272-vs-16504-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504-em.sav 
EM estimation for the following files
SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1/C2C12-myocyte-MEF2-37C-5273-IP-F3-5272-16272.mm10.36mers.unique_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.regionPeak
SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2/C2C12-60h-MEF2-B4-37oC-5404-5406-IP-3F-16504.mm10.36mers.unique_VS_C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.regionPeak
$p
[1] 0.4609565

$rho1
[1] 0.8000996

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504-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] 17351.56

$x.mean2
[1] 37011.96

$y.mean1
[1] 17306.16

$y.mean2
[1] 37050.8

$x.sd1
[1] 13054.52

$x.sd2
[1] 12607.26

$y.sd1
[1] 13421.47

$y.sd2
[1] 12210.75