is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1496729280/PeakSeq-CTCF-GM12878-Rep1.relaxed.narrowPeak_1496729280 :  86757 peaks
 86583 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1496729280/PeakSeq-CTCF-GM12878-Rep2.relaxed.narrowPeak_1496729280 :  89051 peaks
 88882  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-CTCF-GM12878-Rep1_VS_PeakSeq-CTCF-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-CTCF-GM12878-Rep1_VS_PeakSeq-CTCF-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1496729280/PeakSeq-CTCF-GM12878-Rep1.relaxed.narrowPeak_1496729280
/nfs/nobackup/ensembl/akundaje/tmp/idr_1496729280/PeakSeq-CTCF-GM12878-Rep2.relaxed.narrowPeak_1496729280
$p
[1] 0.7660743

$rho1
[1] 0.9678963

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-CTCF-GM12878-Rep1_VS_PeakSeq-CTCF-GM12878-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] 30089.65

$x.mean2
[1] 49725.55

$y.mean1
[1] 28717.91

$y.mean2
[1] 54208.22

$x.sd1
[1] 17789.93

$x.sd2
[1] 19545.45

$y.sd1
[1] 17709.01

$y.sd2
[1] 13752.27