is.broadpeak FALSE 
[1] "Fix 4 stops\n"
[1] "Fix 7 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_64351042/GEMv2-GABP-HELAS3-Rep1.relaxed.narrowPeak_64351042 :  6424 peaks
 6424 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_64351042/GEMv2-GABP-HELAS3-Rep2.relaxed.narrowPeak_64351042 :  7481 peaks
 7481  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/GEMv2/idr/GEMv2-GABP-HELAS3-Rep1_VS_GEMv2-GABP-HELAS3-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-GABP-HELAS3-Rep1_VS_GEMv2-GABP-HELAS3-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_64351042/GEMv2-GABP-HELAS3-Rep1.relaxed.narrowPeak_64351042
/nfs/nobackup/ensembl/akundaje/tmp/idr_64351042/GEMv2-GABP-HELAS3-Rep2.relaxed.narrowPeak_64351042
$p
[1] 0.9186587

$rho1
[1] 0.9259682

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-GABP-HELAS3-Rep1_VS_GEMv2-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] 1997.58

$x.mean2
[1] 2813.598

$y.mean1
[1] 1987.333

$y.mean2
[1] 2915.704

$x.sd1
[1] 1195.694

$x.sd2
[1] 916.6286

$y.sd1
[1] 1193.423

$y.sd2
[1] 846.2629