is.broadpeak FALSE 
[1] "Fix 2 stops\n"
read SPP-300K-HepG2-CTCF-Broad-PooledPseudoRep1/HepG2-CTCF-Broad.ChIP.pooled.sorted.pseudoRep1_VS_HepG2-CTCF-Broad.Control.pooled.sorted.pseudoRep1.regionPeak :  165935 peaks
 165935 peaks are left after cleaning
 SPP-300K-HepG2-CTCF-Broad-PooledPseudoRep2/HepG2-CTCF-Broad.ChIP.pooled.sorted.pseudoRep2_VS_HepG2-CTCF-Broad.Control.pooled.sorted.pseudoRep2.regionPeak :  166219 peaks
 166219  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-HepG2-CTCF-Broad-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-HepG2-CTCF-Broad-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-HepG2-CTCF-Broad-PooledPseudoRep1/HepG2-CTCF-Broad.ChIP.pooled.sorted.pseudoRep1_VS_HepG2-CTCF-Broad.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-HepG2-CTCF-Broad-PooledPseudoRep2/HepG2-CTCF-Broad.ChIP.pooled.sorted.pseudoRep2_VS_HepG2-CTCF-Broad.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.7182741

$rho1
[1] 0.9415676

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-HepG2-CTCF-Broad-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] 26814.43

$x.mean2
[1] 56365.89

$y.mean1
[1] 26844.46

$y.mean2
[1] 56289.42

$x.sd1
[1] 17014.88

$x.sd2
[1] 9782.084

$y.sd1
[1] 17050.06

$y.sd2
[1] 9856.472