is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2503214267/SPP-ZNF274-K562-Rep2.relaxed.narrowPeak_2503214267 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2503214267/SPP-ZNF274-K562-Rep1.relaxed.narrowPeak_2503214267 :  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-ZNF274-K562-Rep2_VS_SPP-ZNF274-K562-Rep1-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/SPP/idr/SPP-ZNF274-K562-Rep2_VS_SPP-ZNF274-K562-Rep1-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2503214267/SPP-ZNF274-K562-Rep2.relaxed.narrowPeak_2503214267
/nfs/nobackup/ensembl/akundaje/tmp/idr_2503214267/SPP-ZNF274-K562-Rep1.relaxed.narrowPeak_2503214267
$p
[1] 0.2096333

$rho1
[1] 0.8351389

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/SPP/idr/SPP-ZNF274-K562-Rep2_VS_SPP-ZNF274-K562-Rep1-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] 4042.898

$x.mean2
[1] 6707.929

$y.mean1
[1] 3667.968

$y.mean2
[1] 6808.785

$x.sd1
[1] 3322.409

$x.sd2
[1] 3388.868

$y.sd1
[1] 3449.918

$y.sd2
[1] 3265.974