is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_417230288/PeakSeq-ZNF274-K562-Rep1.relaxed.narrowPeak_417230288 :  9234 peaks
 9100 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_417230288/PeakSeq-ZNF274-K562-Rep2.relaxed.narrowPeak_417230288 :  31267 peaks
 30962  peaks are left after cleaninghalf.width= reported 
significant measure= q.value 
URI is done
URI is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-ZNF274-K562-Rep1_VS_PeakSeq-ZNF274-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-ZNF274-K562-Rep1_VS_PeakSeq-ZNF274-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_417230288/PeakSeq-ZNF274-K562-Rep1.relaxed.narrowPeak_417230288
/nfs/nobackup/ensembl/akundaje/tmp/idr_417230288/PeakSeq-ZNF274-K562-Rep2.relaxed.narrowPeak_417230288
$p
[1] 0.4343186

$rho1
[1] 0.9253386

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-ZNF274-K562-Rep1_VS_PeakSeq-ZNF274-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] 670.7222

$x.mean2
[1] 1252.522

$y.mean1
[1] 793.0528

$y.mean2
[1] 1157.394

$x.sd1
[1] 548.7126

$x.sd2
[1] 456.5158

$y.sd1
[1] 572.9763

$y.sd2
[1] 526.5421