is.broadpeak FALSE 
[1] "Fix 12 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_167512012/GEM-ZNF274-K562-Rep1.relaxed.narrowPeak_167512012 :  15086 peaks
 15086 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_167512012/GEM-ZNF274-K562-Rep2.relaxed.narrowPeak_167512012 :  39835 peaks
 39835  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/GEM/idr/GEM-ZNF274-K562-Rep1_VS_GEM-ZNF274-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-ZNF274-K562-Rep1_VS_GEM-ZNF274-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_167512012/GEM-ZNF274-K562-Rep1.relaxed.narrowPeak_167512012
/nfs/nobackup/ensembl/akundaje/tmp/idr_167512012/GEM-ZNF274-K562-Rep2.relaxed.narrowPeak_167512012
$p
[1] 0.5949062

$rho1
[1] 0.8636944

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-ZNF274-K562-Rep1_VS_GEM-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] 759.3927

$x.mean2
[1] 1146.276

$y.mean1
[1] 848.2007

$y.mean2
[1] 1018.477

$x.sd1
[1] 534.7038

$x.sd2
[1] 431.154

$y.sd1
[1] 569.8645

$y.sd2
[1] 448.5636