is.broadpeak FALSE 
[1] "Fix 4 stops\n"
[1] "Fix 9 stops\n"
read SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1/C2C12-60h-Mef2C-37oC-5404-5406-IP-3B-16500.mm10.36mers.unique_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2/C2C12-60h-Mef2C-H180-37oC-5453-IP-C2-16643.mm10.36mers.unique_VS_C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.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-C2C12-60h-Mef2C-37C-16500-vs-16643-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643-em.sav 
EM estimation for the following files
SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1/C2C12-60h-Mef2C-37oC-5404-5406-IP-3B-16500.mm10.36mers.unique_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.regionPeak
SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2/C2C12-60h-Mef2C-H180-37oC-5453-IP-C2-16643.mm10.36mers.unique_VS_C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.regionPeak
$p
[1] 0.2589425

$rho1
[1] 0.09487217

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643-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] 9877.939

$x.mean2
[1] 12238.75

$y.mean1
[1] 10709.13

$y.mean2
[1] 11946.75

$x.sd1
[1] 7204.02

$x.sd2
[1] 6416.811

$y.sd1
[1] 7455.689

$y.sd2
[1] 6397.665