is.broadpeak FALSE 
[1] "Fix 2 stops\n"
[1] "Fix 5 stops\n"
read SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep1/C2C12-exp-MyoD-5273-IP-B4-16265.mm10.36mers.unique_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep2/C2C12-exp-MyoD-5273-IP-C4-16266.mm10.36mers.unique_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.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-MyoD-16265-vs-16266-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-em.sav 
EM estimation for the following files
SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep1/C2C12-exp-MyoD-5273-IP-B4-16265.mm10.36mers.unique_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.regionPeak
SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep2/C2C12-exp-MyoD-5273-IP-C4-16266.mm10.36mers.unique_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.regionPeak
$p
[1] 0.3640472

$rho1
[1] 0.921853

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-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] 14052.64

$x.mean2
[1] 34293.09

$y.mean1
[1] 13582.55

$y.mean2
[1] 34562.49

$x.sd1
[1] 12471.93

$x.sd2
[1] 11894.21

$y.sd1
[1] 11530.94

$y.sd2
[1] 11971.26