processor ID: 26020
==========================================================================

|------------------------------------------------------------------|
|                                                                  |
|              *** Running a seeded analysis ***                   |
|                                                                  |
|------------------------------------------------------------------|

command line: /home/grobertson/Fi/Code/20090926_v1.3/Fi_v1.3/bin/fi -fseq /projects/remc_bigdata/Karsan/HS1238_kd/compare/FA/HS1238-compare-p1em6_9461-selfUnion-pm500bp-rgns.hg18.fa.3stage_dm_w4.fa -fout /projects/remc_bigdata/Karsan/HS1238_kd/compare/seed_NFkB_M00280/c/HS1238-compare-p1em6_9461-selfUnion-pm500bp-rgns.hg18.fa.3stage_dm_w4.fa.pwmNFkB_M00208.mx.weight0.minn500.de_novo -minN 500 -ev 5000 -pv 0.0002 -fpwm0 /home/grobertson/Fi/PWMs/NFkB_M00208.mx -em 80 -fEM 0.5 -posWt 0 -extTrim EXTRIM -verbose 1 -pgf 0 -fbm /home/grobertson/Fi/Code/20090926_v1.3/KmerFreq/hg18_kmer_1to9_freq.txt -bOrder 3 

maximal buffer length:					15000
maximal number of sequences set:			100000
maximal number of bases per seq read:			20000
maximal number of sites in a motif:			150000
input (ChIP) sequence file:				/projects/remc_bigdata/Karsan/HS1238_kd/compare/FA/HS1238-compare-p1em6_9461-selfUnion-pm500bp-rgns.hg18.fa.3stage_dm_w4.fa
number of sequences in input file:			9461
average sequence length:				1071
total number of nucleotides:				10140208
max number of generations:				1
population size:					10
use a user-specified pwm as the seed			/home/grobertson/Fi/PWMs/NFkB_M00208.mx
fraction (number) input sequences subject to EM		1.00 (9461)
scale factor for converting (double)pwm to (int)pwm	 200
number of EM steps:					80
EM convergence criterion:				1.000000e-04
run EM on the starting pwm /home/grobertson/Fi/PWMs/NFkB_M00208.mx 10 times, each with a different maxp:
0.10*numSeq 0.20*numSeq 0.30*numSeq 0.40*numSeq 0.50*numSeq 0.60*numSeq 0.70*numSeq 0.80*numSeq 0.90*numSeq 1.00*numSeq 
no spaced dyads are generated and used. pop=10 gen=1 (no GA).

motif prior probability type (see documentation):	0
pwm score p-value cutoff for declaring binding site:	2.000000e-04

Approximate the null llr log{p(s|M)/p(s|B)} score distribution using
the llr scores of random/background sequences, where M is the EM-derived
motif model and B is the 3-th order Markov backgroun model.

The background sequences are simulated using the [a,c,g,t] frequencies
in the input data. The number sets of background sequences generated: 	10

pseudo count:						0.0005
minimal infomation for trimming/extending: 		0.40 0.50 0.60
minimal no. sites for each motif:			500
base extension and trimming? 				no
sliding window for comparing pwm similarity:	6
PWM similarity cutoff:					0.300
log(E-value) cutoff:					5000.00
number of adjacent bases included in binding site output:	10

job started: Sun Jul 11 21:14:11 2010

=========================================================================

GADEM cycle[  1] generation[  1] number of unique motif(s): 2
   spacedDyad: rGGGAyTTTCCm         motifConsensus: TTyyyTyyyyyy          1.00 fitness: -1888.51
   spacedDyad: rGGGAyTTTCCm         motifConsensus: AGyGATyCTCCy          0.40 fitness:  449.02

GADEM cycle[  2] generation[  1] number of unique motif(s): 3
   spacedDyad: rGGGAyTTTCCm         motifConsensus: TCnGCCTCCyrr          0.70 fitness: -12093.76
   spacedDyad: rGGGAyTTTCCm         motifConsensus: AAAAATACAAAA          0.10 fitness: -1929.69
   spacedDyad: rGGGAyTTTCCm         motifConsensus: rGrGTyTCrCym          0.40 fitness: 1604.88

GADEM cycle[  3] generation[  1] number of unique motif(s): 1
   spacedDyad: rGGGAyTTTCCm         motifConsensus: wwwwywTTTwww          0.90 fitness: 2656.55

GADEM cycle[  4] generation[  1] number of unique motif(s): 1
   spacedDyad: rGGGAyTTTCCm         motifConsensus: nkGCyyyyyyCh          0.40 fitness: 2133.30

GADEM cycle[  5] generation[  1] number of unique motif(s): 1
   spacedDyad: rGGGAyTTTCCm         motifConsensus: wyTswkTTyyyw          0.80 fitness: 3341.00

GADEM cycle[  6] generation[  1] number of unique motif(s): 1
   spacedDyad: rGGGAyTTTCCm         motifConsensus: wrrmAnTTyyyw          0.50 fitness: 4581.20

GADEM cycle[  7] generation[  1] number of unique motif(s): 3
   spacedDyad: rGGGAyTTTCCm         motifConsensus: TyrsCCAGGCTG          0.50 fitness: -8185.07
   spacedDyad: rGGGAyTTTCCm         motifConsensus: mCTGCACTCCAG          0.40 fitness:  -84.46
   spacedDyad: rGGGAyTTTCCm         motifConsensus: dGrGsCwGGsws          0.90 fitness: 2067.05

GADEM cycle[  8] generation[  1] number of unique motif(s): 2
   spacedDyad: rGGGAyTTTCCm         motifConsensus: CTGTArTCCCAG          0.70 fitness: -12379.07
   spacedDyad: rGGGAyTTTCCm         motifConsensus: kswGshyyyCwG          0.50 fitness: 2775.42

GADEM cycle[  9] generation[  1] number of unique motif(s): 4
   spacedDyad: rGGGAyTTTCCm         motifConsensus: yrnsyCACTGCA          0.80 fitness: -1240.16
   spacedDyad: rGGGAyTTTCCm         motifConsensus: TGAGCCACCryr          0.10 fitness: -300.51
   spacedDyad: rGGGAyTTTCCm         motifConsensus: nywbChTyyyCw          1.00 fitness: 2810.96
   spacedDyad: rGGGAyTTTCCm         motifConsensus: nnyCCCAsCyCm          0.40 fitness: 3285.16

GADEM cycle[ 10] generation[  1] number of unique motif(s): 1
   spacedDyad: rGGGAyTTTCCm         motifConsensus: wkddnwTTTrmA          0.40 fitness: 4786.41


finished: Mon Jul 12 21:25:10 2010

approximated processor time in seconds: 87059.000000