is.broadpeak FALSE 
read SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep1PseudoRep1/A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep1_VS_A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep1.regionPeak :  43346 peaks
 43346 peaks are left after cleaning
 SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep1PseudoRep2/A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep2_VS_A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep2.regionPeak :  51328 peaks
 51328  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-Rep1PseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep1PseudoReps-em.sav 
EM estimation for the following files
SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep1PseudoRep1/A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep1_VS_A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep1.regionPeak
SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep1PseudoRep2/A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep2_VS_A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep2.regionPeak
$p
[1] 0.5833243

$rho1
[1] 0.2629368

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-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] 10171.96

$x.mean2
[1] 10457.37

$y.mean1
[1] 9805.229

$y.mean2
[1] 10969.93

$x.sd1
[1] 6470.906

$x.sd2
[1] 5103.816

$y.sd1
[1] 6368.704

$y.sd2
[1] 5209.578