is.broadpeak FALSE 
[1] "Fix 13 stops\n"
[1] "Fix 22 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_272498865/GEMv2-P300-K562-Rep1.relaxed.narrowPeak_272498865 :  17966 peaks
 17966 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_272498865/GEMv2-P300-K562-Rep2.relaxed.narrowPeak_272498865 :  31664 peaks
 31664  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-P300-K562-Rep1_VS_GEMv2-P300-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-P300-K562-Rep1_VS_GEMv2-P300-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_272498865/GEMv2-P300-K562-Rep1.relaxed.narrowPeak_272498865
/nfs/nobackup/ensembl/akundaje/tmp/idr_272498865/GEMv2-P300-K562-Rep2.relaxed.narrowPeak_272498865
$p
[1] 0.720933

$rho1
[1] 0.8096026

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-P300-K562-Rep1_VS_GEMv2-P300-K562-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] 5204.649

$x.mean2
[1] 5846.248

$y.mean1
[1] 5109.853

$y.mean2
[1] 6088.686

$x.sd1
[1] 3234.494

$x.sd2
[1] 2707.232

$y.sd1
[1] 3253.509

$y.sd2
[1] 2573.08