is.broadpeak FALSE 
read SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-PooledPseudoRep1/IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.ChIP.pooled.sorted.pseudoRep1_VS_IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.Control.pooled.sorted.pseudoRep1.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-PooledPseudoRep2/IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.ChIP.pooled.sorted.pseudoRep2_VS_IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.Control.pooled.sorted.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-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-PooledPseudoRep1/IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.ChIP.pooled.sorted.pseudoRep1_VS_IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-PooledPseudoRep2/IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.ChIP.pooled.sorted.pseudoRep2_VS_IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.4769195

$rho1
[1] 0.05055699

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-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] 16505.08

$x.mean2
[1] 20325.06

$y.mean1
[1] 17033.84

$y.mean2
[1] 19842.84

$x.sd1
[1] 10944.58

$x.sd2
[1] 10095.88

$y.sd1
[1] 10986.44

$y.sd2
[1] 10212.06