is.broadpeak FALSE 
[1] "Fix 2 stops\n"
read SPP-300K-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoRep1/C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-exp-MyoD-16265-vs-16266.Control.pooled.sorted.pseudoRep1.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoRep2/C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-exp-MyoD-16265-vs-16266.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-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoRep1/C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-exp-MyoD-16265-vs-16266.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoRep2/C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-exp-MyoD-16265-vs-16266.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.3788025

$rho1
[1] 0.9319426

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-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] 15661.96

$x.mean2
[1] 38054.38

$y.mean1
[1] 15735.21

$y.mean2
[1] 38009.67

$x.sd1
[1] 13301.86

$x.sd2
[1] 13079.99

$y.sd1
[1] 13425.52

$y.sd2
[1] 13079.21