is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1/C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak :  1672 peaks
 1672 peaks are left after cleaning
 SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2/C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak :  74391 peaks
 74391  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-em.sav 
EM estimation for the following files
SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1/C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak
SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2/C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak
$p
[1] 0.5015313

$rho1
[1] 0.8838966

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-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] 480.8321

$x.mean2
[1] 741.9464

$y.mean1
[1] 481.5371

$y.mean2
[1] 741.2374

$x.sd1
[1] 344.7182

$x.sd2
[1] 310.1728

$y.sd1
[1] 347.2048

$y.sd2
[1] 307.971