is.broadpeak FALSE 
read SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep1/A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique_VS_A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep2/A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique_VS_A549-EtOH-GR-Rep2-GSM2095221.hg20-male.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-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-uri.sav 
EM is done

EM is saved at: IDR-SPP-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-em.sav 
EM estimation for the following files
SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep1/A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique_VS_A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.regionPeak
SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep2/A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique_VS_A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.regionPeak
$p
[1] 0.332696

$rho1
[1] 0.09309237

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-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] 13283.03

$x.mean2
[1] 15542.47

$y.mean1
[1] 13850.9

$y.mean2
[1] 15258.63

$x.sd1
[1] 9013.009

$x.sd2
[1] 8186.352

$y.sd1
[1] 8775.705

$y.sd2
[1] 8376.588