is.broadpeak FALSE 
read SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-PooledPseudoRep1/IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.ChIP.pooled.sorted.pseudoRep1_VS_IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.Control.pooled.sorted.pseudoRep1.regionPeak :  106613 peaks
 106613 peaks are left after cleaning
 SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-PooledPseudoRep2/IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.ChIP.pooled.sorted.pseudoRep2_VS_IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.Control.pooled.sorted.pseudoRep2.regionPeak :  112365 peaks
 112365  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-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-PooledPseudoRep1/IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.ChIP.pooled.sorted.pseudoRep1_VS_IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-PooledPseudoRep2/IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.ChIP.pooled.sorted.pseudoRep2_VS_IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.6010517

$rho1
[1] 0.9324645

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-PooledPseudoReps-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] 9039.953

$x.mean2
[1] 19367.36

$y.mean1
[1] 9025.531

$y.mean2
[1] 19389.05

$x.sd1
[1] 6232.513

$x.sd2
[1] 4702.546

$y.sd1
[1] 6205.661

$y.sd2
[1] 4708.235