is.broadpeak FALSE 
[1] "Fix 9 stops\n"
[1] "Fix 1 stops\n"
read SPP-300K-K562-CTCF-HA-Rep1/K562-CTCF-Rep1-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V2-Rep2-HA.hg20-female.36mers.unique.regionPeak :  239349 peaks
 239349 peaks are left after cleaning
 SPP-300K-K562-CTCF-HA-Rep2/K562-CTCF-Rep2-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V2-Rep2-HA.hg20-female.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-K562-CTCF-HA-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-CTCF-HA-em.sav 
EM estimation for the following files
SPP-300K-K562-CTCF-HA-Rep1/K562-CTCF-Rep1-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V2-Rep2-HA.hg20-female.36mers.unique.regionPeak
SPP-300K-K562-CTCF-HA-Rep2/K562-CTCF-Rep2-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V2-Rep2-HA.hg20-female.36mers.unique.regionPeak
$p
[1] 0.6547797

$rho1
[1] 0.8708909

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-CTCF-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] 27002.88

$x.mean2
[1] 55907.87

$y.mean1
[1] 27452.76

$y.mean2
[1] 55055.38

$x.sd1
[1] 18078.85

$x.sd2
[1] 12389.03

$y.sd1
[1] 17859.69

$y.sd2
[1] 14716.85