is.broadpeak FALSE 
[1] "Fix 2 stops\n"
[1] "Fix 3 stops\n"
read SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoRep1/C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.sorted.pseudoRep1.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoRep2/C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-exp-MEF2-B4-37C-16503-vs-16645.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-MEF2-B4-37C-16503-vs-16645-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoRep1/C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoRep2/C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.4055821

$rho1
[1] 0.8734935

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-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] 17589.68

$x.mean2
[1] 39768.03

$y.mean1
[1] 17522.71

$y.mean2
[1] 39813.76

$x.sd1
[1] 14450.62

$x.sd2
[1] 13738.07

$y.sd1
[1] 14412.05

$y.sd2
[1] 13691.65