is.broadpeak FALSE 
[1] "Fix 2 stops\n"
[1] "Fix 1 stops\n"
read SPP-300K-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-PooledPseudoRep1/G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI.ChIP.pooled.sorted.pseudoRep1_VS_G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI.Control.pooled.sorted.pseudoRep1.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-PooledPseudoRep2/G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI.ChIP.pooled.sorted.pseudoRep2_VS_G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI.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-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-PooledPseudoReps-uri.sav 
EM is done

EM is saved at: IDR-SPP-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-PooledPseudoReps-em.sav 
EM estimation for the following files
SPP-300K-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-PooledPseudoRep1/G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI.ChIP.pooled.sorted.pseudoRep1_VS_G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI.Control.pooled.sorted.pseudoRep1.regionPeak
SPP-300K-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-PooledPseudoRep2/G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI.ChIP.pooled.sorted.pseudoRep2_VS_G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI.Control.pooled.sorted.pseudoRep2.regionPeak
$p
[1] 0.1676091

$rho1
[1] 0.6251351

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-G1E-ER4-24h-GATA2-ENCFF001MSD-vs-ENCFF001MSI-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] 21925.61

$x.mean2
[1] 30110.02

$y.mean1
[1] 21979.74

$y.mean2
[1] 30099.07

$x.sd1
[1] 16158.13

$x.sd2
[1] 16330.59

$y.sd1
[1] 16375.33

$y.sd2
[1] 16292.26