is.broadpeak FALSE 
[1] "Fix 3 stops\n"
read SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoRep1/G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep1_VS_G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.sorted.pseudoRep1.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoRep2/G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep2_VS_G1E-CTCF-Rep1-vs-Rep2-PSU.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-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoRep1/G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep1_VS_G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoRep2/G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep2_VS_G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.3326843

$rho1
[1] 0.8960129

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU-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] 15812.57

$x.mean2
[1] 40723.35

$y.mean1
[1] 14954

$y.mean2
[1] 41151.88

$x.sd1
[1] 14734.46

$x.sd2
[1] 14504.87

$y.sd1
[1] 13535.52

$y.sd2
[1] 14332.02