is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep1/C2C12-myocyte-myogenin-RT-5273-IP-E4-5261-16273.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak :  49589 peaks
 49589 peaks are left after cleaning
 SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep2/C2C12-60h-myogenin-RT-5199-5406-IP-2C-16495.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak :  35162 peaks
 35162  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-em.sav 
EM estimation for the following files
SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep1/C2C12-myocyte-myogenin-RT-5273-IP-E4-5261-16273.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak
SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep2/C2C12-60h-myogenin-RT-5199-5406-IP-2C-16495.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak
$p
[1] 0.6386038

$rho1
[1] 0.9481504

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-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] 10407.51

$x.mean2
[1] 21382.23

$y.mean1
[1] 10347.37

$y.mean2
[1] 21488.26

$x.sd1
[1] 7122.482

$x.sd2
[1] 4906.93

$y.sd1
[1] 7048.627

$y.sd2
[1] 4855.769