is.broadpeak FALSE 
[1] "Fix 14 stops\n"
read SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep1/C2C12-24h-MyoD-10008-1pFA.mm10.36mers.unique_VS_C2C12-24h-2PCR-Input-10007-1pFA.mm10.36mers.unique.regionPeak :  72018 peaks
 72018 peaks are left after cleaning
 SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep2/C2C12-24h-MyoD-10296-1pFA.mm10.36mers.unique_VS_C2C12-24h-2PCR-Input-10391-1pFA.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_MyoD_24h_10008-vs-10296-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12_MyoD_24h_10008-vs-10296-em.sav 
EM estimation for the following files
SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep1/C2C12-24h-MyoD-10008-1pFA.mm10.36mers.unique_VS_C2C12-24h-2PCR-Input-10007-1pFA.mm10.36mers.unique.regionPeak
SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep2/C2C12-24h-MyoD-10296-1pFA.mm10.36mers.unique_VS_C2C12-24h-2PCR-Input-10391-1pFA.mm10.36mers.unique.regionPeak
$p
[1] 0.5931158

$rho1
[1] 0.8786672

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12_MyoD_24h_10008-vs-10296-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] 12685.77

$x.mean2
[1] 25522.11

$y.mean1
[1] 13390.59

$y.mean2
[1] 24495.79

$x.sd1
[1] 8958.624

$x.sd2
[1] 6931.732

$y.sd1
[1] 9331.882

$y.sd2
[1] 7917.038