is.broadpeak FALSE 
read SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoRep1/C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted.pseudoRep1.regionPeak :  9055 peaks
 9055 peaks are left after cleaning
 SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoRep2/C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted.pseudoRep2.regionPeak :  9012 peaks
 9012  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-16502-vs-16503-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoRep1/C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoRep2/C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.5367367

$rho1
[1] 0.8893521

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-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] 2130.709

$x.mean2
[1] 3979.953

$y.mean1
[1] 2182.538

$y.mean2
[1] 3920.05

$x.sd1
[1] 1565.609

$x.sd2
[1] 1323.376

$y.sd1
[1] 1617.392

$y.sd2
[1] 1332.546