is.broadpeak FALSE 
[1] "Fix 1 stops\n"
[1] "Fix 4 stops\n"
read SPP-300K-K562-CTCF-HA-PooledPseudoRep1/K562-CTCF-HA.ChIP.pooled.sorted.pseudoRep1_VS_K562-CTCF-HA.Control.pooled.sorted.pseudoRep1.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-K562-CTCF-HA-PooledPseudoRep2/K562-CTCF-HA.ChIP.pooled.sorted.pseudoRep2_VS_K562-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-K562-CTCF-HA-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-CTCF-HA-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-K562-CTCF-HA-PooledPseudoRep1/K562-CTCF-HA.ChIP.pooled.sorted.pseudoRep1_VS_K562-CTCF-HA.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-K562-CTCF-HA-PooledPseudoRep2/K562-CTCF-HA.ChIP.pooled.sorted.pseudoRep2_VS_K562-CTCF-HA.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.5065488

$rho1
[1] 0.9754923

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-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] 31200.29

$x.mean2
[1] 78601.99

$y.mean1
[1] 31263.57

$y.mean2
[1] 78537.03

$x.sd1
[1] 22528.54

$x.sd2
[1] 18796.57

$y.sd1
[1] 22615.38

$y.sd2
[1] 18853.02