is.broadpeak FALSE 
[1] "Fix 4 stops\n"
[1] "Fix 4 stops\n"
read SPP-300K-K562-CTCF-Broad-Rep1/K562-CTCF-Rep1-Broad.hg20-female.36mers.unique_VS_K562-Control-Rep1-Broad.hg20-female.36mers.unique.regionPeak :  232591 peaks
 232591 peaks are left after cleaning
 SPP-300K-K562-CTCF-Broad-Rep2/K562-CTCF-Rep2-Broad.hg20-female.36mers.unique_VS_K562-Control-Rep1-Broad.hg20-female.36mers.unique.regionPeak :  279669 peaks
 279669  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-K562-CTCF-Broad-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-CTCF-Broad-em.sav 
EM estimation for the following files
SPP-300K-K562-CTCF-Broad-Rep1/K562-CTCF-Rep1-Broad.hg20-female.36mers.unique_VS_K562-Control-Rep1-Broad.hg20-female.36mers.unique.regionPeak
SPP-300K-K562-CTCF-Broad-Rep2/K562-CTCF-Rep2-Broad.hg20-female.36mers.unique_VS_K562-Control-Rep1-Broad.hg20-female.36mers.unique.regionPeak
$p
[1] 0.6418709

$rho1
[1] 0.9283281

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-CTCF-Broad-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] 31601.34

$x.mean2
[1] 69355.14

$y.mean1
[1] 31873.58

$y.mean2
[1] 68867.54

$x.sd1
[1] 20900.71

$x.sd2
[1] 14035.51

$y.sd1
[1] 21183.17

$y.sd2
[1] 14565.46