is.broadpeak FALSE 
read SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep1PseudoRep1/A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep1_VS_A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep1.regionPeak :  19491 peaks
 19491 peaks are left after cleaning
 SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep1PseudoRep2/A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep2_VS_A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep2.regionPeak :  14270 peaks
 14270  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-Rep1PseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep1PseudoReps-em.sav 
EM estimation for the following files
SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep1PseudoRep1/A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep1_VS_A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep1.regionPeak
SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep1PseudoRep2/A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep2_VS_A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep2.regionPeak
$p
[1] 0.2782916

$rho1
[1] 0.9604969

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep1PseudoReps-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] 1584.793

$x.mean2
[1] 3033.754

$y.mean1
[1] 1579.218

$y.mean2
[1] 3035.948

$x.sd1
[1] 1451.562

$x.sd2
[1] 1332.601

$y.sd1
[1] 1465.412

$y.sd2
[1] 1324.216