is.broadpeak FALSE 
read SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep1/A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep1_VS_A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.pseudoRep1.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep2/A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep2_VS_A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.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-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep1/A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep1_VS_A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep2/A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep2_VS_A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.4758571

$rho1
[1] 0.9762819

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-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] 26277.74

$x.mean2
[1] 69879.08

$y.mean1
[1] 26106.11

$y.mean2
[1] 70034.91

$x.sd1
[1] 19349.1

$x.sd2
[1] 17029.39

$y.sd1
[1] 18967.05

$y.sd2
[1] 17019.14