is.broadpeak FALSE 
[1] "Fix 2 stops\n"
read SPP-300K-K562-MAX-SYDH-PooledPseudoRep1/K562-MAX-SYDH.ChIP.pooled.sorted.pseudoRep1_VS_K562-MAX-SYDH.Control.pooled.sorted.pseudoRep1.regionPeak :  104519 peaks
 104519 peaks are left after cleaning
 SPP-300K-K562-MAX-SYDH-PooledPseudoRep2/K562-MAX-SYDH.ChIP.pooled.sorted.pseudoRep2_VS_K562-MAX-SYDH.Control.pooled.sorted.pseudoRep2.regionPeak :  104330 peaks
 104330  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-K562-MAX-SYDH-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-MAX-SYDH-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-K562-MAX-SYDH-PooledPseudoRep1/K562-MAX-SYDH.ChIP.pooled.sorted.pseudoRep1_VS_K562-MAX-SYDH.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-K562-MAX-SYDH-PooledPseudoRep2/K562-MAX-SYDH.ChIP.pooled.sorted.pseudoRep2_VS_K562-MAX-SYDH.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.447107

$rho1
[1] 0.885738

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-MAX-SYDH-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] 7511.095

$x.mean2
[1] 14250.18

$y.mean1
[1] 7589.62

$y.mean2
[1] 14186.62

$x.sd1
[1] 5877.829

$x.sd2
[1] 5276.117

$y.sd1
[1] 5925.145

$y.sd2
[1] 5313.475