is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep1/C2C12-60h-MyoD-60-min-16058.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak :  50397 peaks
 50397 peaks are left after cleaning
 SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep2/C2C12-60h-MyoD-75-min-16059.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak :  160231 peaks
 160231  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-em.sav 
EM estimation for the following files
SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep1/C2C12-60h-MyoD-60-min-16058.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak
SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep2/C2C12-60h-MyoD-75-min-16059.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak
$p
[1] 0.5887449

$rho1
[1] 0.924923

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-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] 8604.455

$x.mean2
[1] 17065.03

$y.mean1
[1] 8563.557

$y.mean2
[1] 17123.49

$x.sd1
[1] 6142.113

$x.sd2
[1] 4715.402

$y.sd1
[1] 6082.858

$y.sd2
[1] 4719.686