processor ID: 23143 ========================================================================== |------------------------------------------------------------------| | | | *** 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_RBPJ_MEME-m1/d/HS1238-compare-p1em6_9461-selfUnion-pm500bp-rgns.hg18.fa.3stage_dm_w4.fa.pwmCSL-MEME-m1.mx.minn1000.weight0.de_novo -minN 1000 -ev 5000 -pv 0.0002 -fpwm0 /home/grobertson/Fi/PWMs/CSL-MEME-m1.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/CSL-MEME-m1.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/CSL-MEME-m1.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: 1000 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 18:56:27 2010 ========================================================================= GADEM cycle[ 1] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: yyTGGGAG 1.00 fitness: -75.84 GADEM cycle[ 2] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: rGAGGsAG 1.00 fitness: -4927.35 GADEM cycle[ 3] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: GsTGGGrk 0.90 fitness: -4051.43 GADEM cycle[ 4] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: AAAGAAAA 0.90 fitness: -2806.63 GADEM cycle[ 5] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: AGrrrAAA 0.90 fitness: 924.64 GADEM cycle[ 6] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: AmTGrAAw 1.00 fitness: 3236.75 spacedDyad: yGTGGGAA motifConsensus: wGTGrrAA 0.30 fitness: 4191.38 GADEM cycle[ 7] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: wGkGGsAr 0.60 fitness: 2370.60 GADEM cycle[ 8] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: wTTTTAAA 0.80 fitness: 2297.37 spacedDyad: yGTGGGAA motifConsensus: rrAGrGAA 0.40 fitness: 3247.48 GADEM cycle[ 9] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CAGGArrh 0.50 fitness: -324.07 spacedDyad: yGTGGGAA motifConsensus: yCwGGAAA 0.80 fitness: 3822.19 GADEM cycle[ 10] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: yyTGrAAA 1.00 fitness: 3386.08 GADEM cycle[ 11] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: vATGrGrA 0.30 fitness: 3545.84 GADEM cycle[ 12] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: TyTsTGAr 0.90 fitness: 3962.56 spacedDyad: yGTGGGAA motifConsensus: AAAATAmA 0.50 fitness: 3970.55 spacedDyad: yGTGGGAA motifConsensus: wTGGwGAA 0.60 fitness: 4337.93 GADEM cycle[ 13] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: rGrsTGAG 0.90 fitness: 1803.08 spacedDyad: yGTGGGAA motifConsensus: krAGrAAA 0.50 fitness: 4311.81 spacedDyad: yGTGGGAA motifConsensus: wATrTrAA 0.80 fitness: 4689.30 GADEM cycle[ 14] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: CwGGAGTk 0.90 fitness: 583.46 spacedDyad: yGTGGGAA motifConsensus: sCAGksAG 1.00 fitness: 1148.50 spacedDyad: yGTGGGAA motifConsensus: CAAGTGAT 0.10 fitness: 3000.86 GADEM cycle[ 15] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: yCTGGGCy 0.60 fitness: 2714.39 GADEM cycle[ 16] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: yCTGkAAT 0.80 fitness: 4495.23 spacedDyad: yGTGGGAA motifConsensus: TyTsTGTy 0.30 fitness: 4679.52 spacedDyad: yGTGGGAA motifConsensus: TyTGkswT 0.60 fitness: 4984.49 GADEM cycle[ 17] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: sAGGrsAG 0.90 fitness: 3590.18 spacedDyad: yGTGGGAA motifConsensus: swGswGAG 0.60 fitness: 3788.39 spacedDyad: yGTGGGAA motifConsensus: sCTkTGAG 0.50 fitness: 4998.02 GADEM cycle[ 18] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: vCTkTGAr 0.60 fitness: 3979.29 finished: Tue Jul 13 04:06:32 2010 approximated processor time in seconds: 119405.000000