is.broadpeak FALSE 
[1] "Fix 4 stops\n"
[1] "Fix 6 stops\n"
read SPP-300K-K562-CTCF-Broad-PooledPseudoRep1/K562-CTCF-Broad.ChIP.pooled.sorted.pseudoRep1_VS_K562-CTCF-Broad.Control.pooled.sorted.pseudoRep1.regionPeak :  273004 peaks
 273004 peaks are left after cleaning
 SPP-300K-K562-CTCF-Broad-PooledPseudoRep2/K562-CTCF-Broad.ChIP.pooled.sorted.pseudoRep2_VS_K562-CTCF-Broad.Control.pooled.sorted.pseudoRep2.regionPeak :  272760 peaks
 272760  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-K562-CTCF-Broad-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-CTCF-Broad-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-K562-CTCF-Broad-PooledPseudoRep1/K562-CTCF-Broad.ChIP.pooled.sorted.pseudoRep1_VS_K562-CTCF-Broad.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-K562-CTCF-Broad-PooledPseudoRep2/K562-CTCF-Broad.ChIP.pooled.sorted.pseudoRep2_VS_K562-CTCF-Broad.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.5904761

$rho1
[1] 0.9541211

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-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] 33902.71

$x.mean2
[1] 77447.15

$y.mean1
[1] 34006.27

$y.mean2
[1] 77297.89

$x.sd1
[1] 23362.51

$x.sd2
[1] 16479.05

$y.sd1
[1] 23487.72

$y.sd2
[1] 16615.21