is.broadpeak FALSE 
[1] "Fix 2 stops\n"
read SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep2PseudoRep1/A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep1_VS_A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep1.regionPeak :  2384 peaks
 2384 peaks are left after cleaning
 SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep2PseudoRep2/A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep2_VS_A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep2.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-Rep2PseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep2PseudoReps-em.sav 
EM estimation for the following files
SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep2PseudoRep1/A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep1_VS_A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep1.regionPeak
SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep2PseudoRep2/A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep2_VS_A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep2.regionPeak
$p
[1] 0.5564141

$rho1
[1] 0.9332774

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-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] 428.3405

$x.mean2
[1] 814.9952

$y.mean1
[1] 424.8502

$y.mean2
[1] 819.2973

$x.sd1
[1] 307.5636

$x.sd2
[1] 265.3687

$y.sd1
[1] 308.1922

$y.sd2
[1] 258.0372