is.broadpeak FALSE 
read SPP-300K-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoRep1/C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted.pseudoRep1.regionPeak :  15677 peaks
 15677 peaks are left after cleaning
 SPP-300K-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoRep2/C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted.pseudoRep2.regionPeak :  15431 peaks
 15431  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoRep1/C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoRep2/C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.6152891

$rho1
[1] 0.9397498

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-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] 4341.779

$x.mean2
[1] 8628.466

$y.mean1
[1] 4356.506

$y.mean2
[1] 8605.007

$x.sd1
[1] 3043.471

$x.sd2
[1] 2239.053

$y.sd1
[1] 3049.093

$y.sd2
[1] 2271.349