is.broadpeak FALSE 
[1] "Fix 48 stops\n"
[1] "Fix 35 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_3178127957/GPSv2-POL2-H1NEURON-Rep1.relaxed.narrowPeak_3178127957 :  47454 peaks
 47454 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_3178127957/GPSv2-POL2-H1NEURON-Rep2.relaxed.narrowPeak_3178127957 :  57822 peaks
 57822  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/GPSv2/idr/GPSv2-POL2-H1NEURON-Rep1_VS_GPSv2-POL2-H1NEURON-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPSv2/idr/GPSv2-POL2-H1NEURON-Rep1_VS_GPSv2-POL2-H1NEURON-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_3178127957/GPSv2-POL2-H1NEURON-Rep1.relaxed.narrowPeak_3178127957
/nfs/nobackup/ensembl/akundaje/tmp/idr_3178127957/GPSv2-POL2-H1NEURON-Rep2.relaxed.narrowPeak_3178127957
$p
[1] 0.8938978

$rho1
[1] 0.8769288

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPSv2/idr/GPSv2-POL2-H1NEURON-Rep1_VS_GPSv2-POL2-H1NEURON-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] 14729.85

$x.mean2
[1] 24778.45

$y.mean1
[1] 14630.58

$y.mean2
[1] 25603.99

$x.sd1
[1] 8863.236

$x.sd2
[1] 5692.21

$y.sd1
[1] 8817.882

$y.sd2
[1] 4659.976