is.broadpeak FALSE 
read SPP-300K-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-PooledPseudoRep1/G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM.ChIP.pooled.sorted.pseudoRep1_VS_G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM.Control.pooled.sorted.pseudoRep1.regionPeak :  192277 peaks
 192277 peaks are left after cleaning
 SPP-300K-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-PooledPseudoRep2/G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM.ChIP.pooled.sorted.pseudoRep2_VS_G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM.Control.pooled.sorted.pseudoRep2.regionPeak :  192541 peaks
 192541  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-PooledPseudoRep1/G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM.ChIP.pooled.sorted.pseudoRep1_VS_G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-PooledPseudoRep2/G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM.ChIP.pooled.sorted.pseudoRep2_VS_G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.2689057

$rho1
[1] 0.9042159

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-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] 5209.566

$x.mean2
[1] 11979.71

$y.mean1
[1] 4944.178

$y.mean2
[1] 12077.89

$x.sd1
[1] 5121.987

$x.sd2
[1] 4996.38

$y.sd1
[1] 4882.229

$y.sd2
[1] 4948.344