is.broadpeak FALSE 
[1] "Fix 1 stops\n"
[1] "Fix 1 stops\n"
read SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep1/A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique_VS_A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep2/A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique_VS_A549-Dex-GR-Rep2-GSM2095219.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-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-uri.sav 
EM is done

EM is saved at: IDR-SPP-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-em.sav 
EM estimation for the following files
SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep1/A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique_VS_A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.regionPeak
SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep2/A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique_VS_A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.regionPeak
$p
[1] 0.4027285

$rho1
[1] 0.9242533

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-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] 14843.26

$x.mean2
[1] 36371.2

$y.mean1
[1] 14907.67

$y.mean2
[1] 36327.74

$x.sd1
[1] 12241.14

$x.sd2
[1] 11844.59

$y.sd1
[1] 12250.72

$y.sd2
[1] 11916.49