is.broadpeak FALSE 
[1] "Fix 9 stops\n"
[1] "Fix 20 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_272909532/GEM-GABP-HELAS3-Rep1.relaxed.narrowPeak_272909532 :  22661 peaks
 22661 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_272909532/GEM-GABP-HELAS3-Rep2.relaxed.narrowPeak_272909532 :  30829 peaks
 30829  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-GABP-HELAS3-Rep1_VS_GEM-GABP-HELAS3-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-GABP-HELAS3-Rep1_VS_GEM-GABP-HELAS3-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_272909532/GEM-GABP-HELAS3-Rep1.relaxed.narrowPeak_272909532
/nfs/nobackup/ensembl/akundaje/tmp/idr_272909532/GEM-GABP-HELAS3-Rep2.relaxed.narrowPeak_272909532
$p
[1] 0.6275157

$rho1
[1] 0.9432258

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-GABP-HELAS3-Rep1_VS_GEM-GABP-HELAS3-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] 3883.625

$x.mean2
[1] 7570.925

$y.mean1
[1] 3937.559

$y.mean2
[1] 7480.528

$x.sd1
[1] 2729.648

$x.sd2
[1] 1919.89

$y.sd1
[1] 2798.035

$y.sd2
[1] 1925.094