is.broadpeak FALSE 
[1] "Fix 4 stops\n"
[1] "Fix 6 stops\n"
read SPP-300K-K562-TEAD4-HA-Rep1/K562-TEAD4-Rep1-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V2-Rep2-HA.hg20-female.36mers.unique.regionPeak :  300000 peaks
 300000 peaks are left after cleaning
 SPP-300K-K562-TEAD4-HA-Rep2/K562-TEAD4-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-TEAD4-HA-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-TEAD4-HA-em.sav 
EM estimation for the following files
SPP-300K-K562-TEAD4-HA-Rep1/K562-TEAD4-Rep1-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V2-Rep2-HA.hg20-female.36mers.unique.regionPeak
SPP-300K-K562-TEAD4-HA-Rep2/K562-TEAD4-Rep2-HA.hg20-female.36mers.unique_VS_K562-1PCR-Input-V2-Rep2-HA.hg20-female.36mers.unique.regionPeak
$p
[1] 0.432235

$rho1
[1] 0.8819961

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-TEAD4-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] 42104.66

$x.mean2
[1] 88705.19

$y.mean1
[1] 44155.75

$y.mean2
[1] 87143.4

$x.sd1
[1] 33859.53

$x.sd2
[1] 30777.91

$y.sd1
[1] 34285.62

$y.sd2
[1] 32635.69