is.broadpeak FALSE 
[1] "Fix 54 stops\n"
[1] "Fix 63 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_97959371/GEMv2-POL2-H1NEURON-Rep1.relaxed.narrowPeak_97959371 :  51479 peaks
 51479 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_97959371/GEMv2-POL2-H1NEURON-Rep2.relaxed.narrowPeak_97959371 :  64346 peaks
 64346  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-POL2-H1NEURON-Rep1_VS_GEMv2-POL2-H1NEURON-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-POL2-H1NEURON-Rep1_VS_GEMv2-POL2-H1NEURON-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_97959371/GEMv2-POL2-H1NEURON-Rep1.relaxed.narrowPeak_97959371
/nfs/nobackup/ensembl/akundaje/tmp/idr_97959371/GEMv2-POL2-H1NEURON-Rep2.relaxed.narrowPeak_97959371
$p
[1] 0.8475411

$rho1
[1] 0.8906024

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-POL2-H1NEURON-Rep1_VS_GEMv2-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] 14352.03

$x.mean2
[1] 23589.51

$y.mean1
[1] 14270.17

$y.mean2
[1] 24040.73

$x.sd1
[1] 8885.832

$x.sd2
[1] 5679.925

$y.sd1
[1] 8858.577

$y.sd2
[1] 5133.279