is.broadpeak FALSE 
[1] "Fix 4 stops\n"
read SPP-300K-HepG2-FOXA1-sc101058-HA-Rep1/HepG2-FOXA1-sc101058-Rep1-HA.hg20-male.36mers.unique_VS_HepG2-1PCR-Input-Rep1-HA.hg20-male.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-HepG2-FOXA1-sc101058-HA-Rep2/HepG2-FOXA1-sc101058-Rep2-HA.hg20-male.36mers.unique_VS_HepG2-1PCR-Input-Rep2-HA.hg20-male.36mers.unique.regionPeak :  300000 peaks
 300000  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-HepG2-FOXA1-sc101058-HA-uri.sav 
EM is done

EM is saved at: IDR-SPP-HepG2-FOXA1-sc101058-HA-em.sav 
EM estimation for the following files
SPP-300K-HepG2-FOXA1-sc101058-HA-Rep1/HepG2-FOXA1-sc101058-Rep1-HA.hg20-male.36mers.unique_VS_HepG2-1PCR-Input-Rep1-HA.hg20-male.36mers.unique.regionPeak
SPP-300K-HepG2-FOXA1-sc101058-HA-Rep2/HepG2-FOXA1-sc101058-Rep2-HA.hg20-male.36mers.unique_VS_HepG2-1PCR-Input-Rep2-HA.hg20-male.36mers.unique.regionPeak
$p
[1] 0.5424724

$rho1
[1] 0.8980256

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-HepG2-FOXA1-sc101058-HA-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] 37508.22

$x.mean2
[1] 72363.81

$y.mean1
[1] 36665.84

$y.mean2
[1] 73362.43

$x.sd1
[1] 26875.25

$x.sd2
[1] 23787.04

$y.sd1
[1] 27069.63

$y.sd2
[1] 21953.12