is.broadpeak FALSE 
read SPP-300K-HepG2-CTCF-HA-PooledPseudoRep1/HepG2-CTCF-HA.ChIP.pooled.sorted.pseudoRep1_VS_HepG2-CTCF-HA.Control.pooled.sorted.pseudoRep1.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-HepG2-CTCF-HA-PooledPseudoRep2/HepG2-CTCF-HA.ChIP.pooled.sorted.pseudoRep2_VS_HepG2-CTCF-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-HepG2-CTCF-HA-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-HepG2-CTCF-HA-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-HepG2-CTCF-HA-PooledPseudoRep1/HepG2-CTCF-HA.ChIP.pooled.sorted.pseudoRep1_VS_HepG2-CTCF-HA.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-HepG2-CTCF-HA-PooledPseudoRep2/HepG2-CTCF-HA.ChIP.pooled.sorted.pseudoRep2_VS_HepG2-CTCF-HA.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.5988581

$rho1
[1] 0.9812184

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-HepG2-CTCF-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] 32780.11

$x.mean2
[1] 77571.07

$y.mean1
[1] 32741.42

$y.mean2
[1] 77628.82

$x.sd1
[1] 21824.77

$x.sd2
[1] 15069.05

$y.sd1
[1] 21806.99

$y.sd2
[1] 14935.04