is.broadpeak FALSE 
[1] "Fix 16 stops\n"
[1] "Fix 22 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2836815608/SPP-POL2-H1NEURON-Rep1.relaxed.narrowPeak_2836815608 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2836815608/SPP-POL2-H1NEURON-Rep2.relaxed.narrowPeak_2836815608 :  125000 peaks
 125000  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/SPP/idr/SPP-POL2-H1NEURON-Rep1_VS_SPP-POL2-H1NEURON-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/SPP/idr/SPP-POL2-H1NEURON-Rep1_VS_SPP-POL2-H1NEURON-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2836815608/SPP-POL2-H1NEURON-Rep1.relaxed.narrowPeak_2836815608
/nfs/nobackup/ensembl/akundaje/tmp/idr_2836815608/SPP-POL2-H1NEURON-Rep2.relaxed.narrowPeak_2836815608
$p
[1] 0.5668175

$rho1
[1] 0.8615946

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/SPP/idr/SPP-POL2-H1NEURON-Rep1_VS_SPP-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] 25007.1

$x.mean2
[1] 51627.45

$y.mean1
[1] 25336.73

$y.mean2
[1] 51196.29

$x.sd1
[1] 17850.22

$x.sd2
[1] 14440.83

$y.sd1
[1] 18035.91

$y.sd2
[1] 14914.73