is.broadpeak FALSE 
[1] "Fix 17 stops\n"
[1] "Fix 25 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_215714398/dPeak-ZNF274-K562-Rep1.relaxed.narrowPeak_215714398 :  104859 peaks
 104859 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_215714398/dPeak-ZNF274-K562-Rep2.relaxed.narrowPeak_215714398 :  123313 peaks
 123313  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/dPeak/idr/dPeak-ZNF274-K562-Rep1_VS_dPeak-ZNF274-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/dPeak/idr/dPeak-ZNF274-K562-Rep1_VS_dPeak-ZNF274-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_215714398/dPeak-ZNF274-K562-Rep1.relaxed.narrowPeak_215714398
/nfs/nobackup/ensembl/akundaje/tmp/idr_215714398/dPeak-ZNF274-K562-Rep2.relaxed.narrowPeak_215714398
$p
[1] 0.2163536

$rho1
[1] 0.7760394

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/dPeak/idr/dPeak-ZNF274-K562-Rep1_VS_dPeak-ZNF274-K562-Rep2-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] 6682.37

$x.mean2
[1] 10202.96

$y.mean1
[1] 6696.85

$y.mean2
[1] 10198.92

$x.sd1
[1] 5462.697

$x.sd2
[1] 5188.867

$y.sd1
[1] 5067.35

$y.sd2
[1] 5302.091