is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep2PseudoRep1/A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep1_VS_A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep1.regionPeak :  42153 peaks
 42153 peaks are left after cleaning
 SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep2PseudoRep2/A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep2_VS_A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep2.regionPeak :  246237 peaks
 246237  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-Rep2PseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep2PseudoReps-em.sav 
EM estimation for the following files
SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep2PseudoRep1/A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep1_VS_A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep1.regionPeak
SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep2PseudoRep2/A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep2_VS_A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep2.regionPeak
$p
[1] 0.5142804

$rho1
[1] 0.03770576

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep2PseudoReps-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] 1863.919

$x.mean2
[1] 1762.289

$y.mean1
[1] 1852.816

$y.mean2
[1] 1774.027

$x.sd1
[1] 1007.542

$x.sd2
[1] 1086.044

$y.sd1
[1] 1029.853

$y.sd2
[1] 1064.684