is.broadpeak FALSE 
[1] "Fix 2 stops\n"
read SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoRep1/G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted.pseudoRep1_VS_G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.sorted.pseudoRep1.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoRep2/G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted.pseudoRep2_VS_G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.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-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoRep1/G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted.pseudoRep1_VS_G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoRep2/G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted.pseudoRep2_VS_G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.3114397

$rho1
[1] 0.168637

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-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] 18630.72

$x.mean2
[1] 22012.85

$y.mean1
[1] 17797.12

$y.mean2
[1] 22390.68

$x.sd1
[1] 12377.63

$x.sd2
[1] 11819.5

$y.sd1
[1] 12303.37

$y.sd2
[1] 11726.8