is.broadpeak FALSE 
read SPP-300K-K562-CTCF-V0416101-HA-PooledPseudoRep1/K562-CTCF-V0416101-HA.ChIP.pooled.sorted.pseudoRep1_VS_K562-CTCF-V0416101-HA.Control.pooled.sorted.pseudoRep1.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-K562-CTCF-V0416101-HA-PooledPseudoRep2/K562-CTCF-V0416101-HA.ChIP.pooled.sorted.pseudoRep2_VS_K562-CTCF-V0416101-HA.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-K562-CTCF-V0416101-HA-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-CTCF-V0416101-HA-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-K562-CTCF-V0416101-HA-PooledPseudoRep1/K562-CTCF-V0416101-HA.ChIP.pooled.sorted.pseudoRep1_VS_K562-CTCF-V0416101-HA.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-K562-CTCF-V0416101-HA-PooledPseudoRep2/K562-CTCF-V0416101-HA.ChIP.pooled.sorted.pseudoRep2_VS_K562-CTCF-V0416101-HA.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.323871

$rho1
[1] 0.9353809

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-CTCF-V0416101-HA-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] 26048.66

$x.mean2
[1] 59599.06

$y.mean1
[1] 26099.31

$y.mean2
[1] 59574.78

$x.sd1
[1] 24647.93

$x.sd2
[1] 22681.76

$y.sd1
[1] 24586.8

$y.sd2
[1] 22749.35