is.broadpeak FALSE 
[1] "Fix 3 stops\n"
read SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1/C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak :  74391 peaks
 74391 peaks are left after cleaning
 SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2/C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.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-exp-MEF2-B4-37C-16503-vs-16645-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-em.sav 
EM estimation for the following files
SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1/C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak
SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2/C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak
$p
[1] 0.5879526

$rho1
[1] 0.8616624

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-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] 8640.305

$x.mean2
[1] 15227.31

$y.mean1
[1] 8385.555

$y.mean2
[1] 15590.23

$x.sd1
[1] 5957.346

$x.sd2
[1] 5306.711

$y.sd1
[1] 6123.827

$y.sd2
[1] 4504.493