is.broadpeak FALSE 
[1] "Fix 1 stops\n"
[1] "Fix 4 stops\n"
read SPP-300K-K562-JunD-IggRabbit-SYDH-PooledPseudoRep1/K562-JunD-IggRabbit-SYDH.ChIP.pooled.sorted.pseudoRep1_VS_K562-JunD-IggRabbit-SYDH.Control.pooled.sorted.pseudoRep1.regionPeak :  169101 peaks
 169101 peaks are left after cleaning
 SPP-300K-K562-JunD-IggRabbit-SYDH-PooledPseudoRep2/K562-JunD-IggRabbit-SYDH.ChIP.pooled.sorted.pseudoRep2_VS_K562-JunD-IggRabbit-SYDH.Control.pooled.sorted.pseudoRep2.regionPeak :  169180 peaks
 169180  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-K562-JunD-IggRabbit-SYDH-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-JunD-IggRabbit-SYDH-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-K562-JunD-IggRabbit-SYDH-PooledPseudoRep1/K562-JunD-IggRabbit-SYDH.ChIP.pooled.sorted.pseudoRep1_VS_K562-JunD-IggRabbit-SYDH.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-K562-JunD-IggRabbit-SYDH-PooledPseudoRep2/K562-JunD-IggRabbit-SYDH.ChIP.pooled.sorted.pseudoRep2_VS_K562-JunD-IggRabbit-SYDH.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.5098814

$rho1
[1] 0.9424118

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-JunD-IggRabbit-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] 30267.8

$x.mean2
[1] 63121.81

$y.mean1
[1] 30238.48

$y.mean2
[1] 63152.31

$x.sd1
[1] 23073.84

$x.sd2
[1] 18912.18

$y.sd1
[1] 23156.9

$y.sd2
[1] 18752.85