is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2522030677/PeakSeq-P300-K562-Rep1.relaxed.narrowPeak_2522030677 :  71330 peaks
 70903 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2522030677/PeakSeq-P300-K562-Rep2.relaxed.narrowPeak_2522030677 :  76481 peaks
 76127  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-P300-K562-Rep1_VS_PeakSeq-P300-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-P300-K562-Rep1_VS_PeakSeq-P300-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2522030677/PeakSeq-P300-K562-Rep1.relaxed.narrowPeak_2522030677
/nfs/nobackup/ensembl/akundaje/tmp/idr_2522030677/PeakSeq-P300-K562-Rep2.relaxed.narrowPeak_2522030677
$p
[1] 0.663987

$rho1
[1] 0.7929065

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-P300-K562-Rep1_VS_PeakSeq-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] 16943.66

$x.mean2
[1] 28005.63

$y.mean1
[1] 17650.96

$y.mean2
[1] 26610.42

$x.sd1
[1] 11290.65

$x.sd2
[1] 9505.15

$y.sd1
[1] 11601.58

$y.sd2
[1] 10209.87