is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_966924488/PeakSeq-GABP-GM12878-Rep1.relaxed.narrowPeak_966924488 :  19066 peaks
 19049 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_966924488/PeakSeq-GABP-GM12878-Rep2.relaxed.narrowPeak_966924488 :  36412 peaks
 36165  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-GABP-GM12878-Rep1_VS_PeakSeq-GABP-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-GABP-GM12878-Rep1_VS_PeakSeq-GABP-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_966924488/PeakSeq-GABP-GM12878-Rep1.relaxed.narrowPeak_966924488
/nfs/nobackup/ensembl/akundaje/tmp/idr_966924488/PeakSeq-GABP-GM12878-Rep2.relaxed.narrowPeak_966924488
$p
[1] 0.4531493

$rho1
[1] 0.9471144

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-GABP-GM12878-Rep1_VS_PeakSeq-GABP-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] 3680.813

$x.mean2
[1] 8416.026

$y.mean1
[1] 3742.914

$y.mean2
[1] 8364.488

$x.sd1
[1] 2935.321

$x.sd2
[1] 2577.561

$y.sd1
[1] 2976.846

$y.sd2
[1] 2631.027