is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read SPP-300K-K562-MAX-SYDH-Rep1/K562-MAX-Rep1-SYDH.hg20-female.27mers.unique_VS_K562-Input-SYDH.hg20-female.27mers.unique.regionPeak :  134922 peaks
 134922 peaks are left after cleaning
 SPP-300K-K562-MAX-SYDH-Rep2/K562-MAX-Rep2-SYDH.hg20-female.27mers.unique_VS_K562-Input-SYDH.hg20-female.27mers.unique.regionPeak :  77162 peaks
 77162  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-K562-MAX-SYDH-uri.sav 
EM is done

EM is saved at: IDR-SPP-K562-MAX-SYDH-em.sav 
EM estimation for the following files
SPP-300K-K562-MAX-SYDH-Rep1/K562-MAX-Rep1-SYDH.hg20-female.27mers.unique_VS_K562-Input-SYDH.hg20-female.27mers.unique.regionPeak
SPP-300K-K562-MAX-SYDH-Rep2/K562-MAX-Rep2-SYDH.hg20-female.27mers.unique_VS_K562-Input-SYDH.hg20-female.27mers.unique.regionPeak
$p
[1] 0.4582814

$rho1
[1] 0.879321

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-K562-MAX-SYDH-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] 7567.396

$x.mean2
[1] 13392.81

$y.mean1
[1] 7345.892

$y.mean2
[1] 13580.34

$x.sd1
[1] 5890.84

$x.sd2
[1] 5079.882

$y.sd1
[1] 5685.372

$y.sd2
[1] 5055.426