processor ID: 25443 ========================================================================== |------------------------------------------------------------------| | | | *** 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/e/HS1238-compare-p1em6_9461-selfUnion-pm500bp-rgns.hg18.fa.3stage_dm_w4.fa.pwmCSL-MEME-m1.mx.minn500.weight0.de_novo -minN 500 -ev 5000 -pv 0.00015 -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: 1.500000e-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 20:50:44 2010 ========================================================================= GADEM cycle[ 1] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: yyTGGGAG 0.80 fitness: -3445.23 GADEM cycle[ 2] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: dGAGGmAG 0.80 fitness: -7128.97 GADEM cycle[ 3] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: AAAAGAAA 1.00 fitness: -3209.06 spacedDyad: yGTGGGAA motifConsensus: GGwGGrGr 0.90 fitness: -2227.11 spacedDyad: yGTGGGAA motifConsensus: GsTGGGrr 0.70 fitness: -2176.05 GADEM cycle[ 4] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: AATAmAAA 0.60 fitness: -757.97 spacedDyad: yGTGGGAA motifConsensus: AAGrGAAA 0.30 fitness: 3206.16 spacedDyad: yGTGGGAA motifConsensus: TGAGGAAA 0.10 fitness: 4867.48 GADEM cycle[ 5] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: wGTGGrrA 0.30 fitness: 1898.13 spacedDyad: yGTGGGAA motifConsensus: TTTwrAAA 1.00 fitness: 1952.96 spacedDyad: yGTGGGAA motifConsensus: AmTGGAAw 0.60 fitness: 2783.20 GADEM cycle[ 6] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: sAGGrsAG 0.90 fitness: 1485.52 spacedDyad: yGTGGGAA motifConsensus: mATGrGAA 0.40 fitness: 3337.41 GADEM cycle[ 7] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TCTswrAA 0.50 fitness: 2037.10 spacedDyad: yGTGGGAA motifConsensus: TyTryAAA 0.20 fitness: 2804.74 GADEM cycle[ 8] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: AGGCTGGr 0.70 fitness: -3177.79 spacedDyad: yGTGGGAA motifConsensus: wGrCwGAG 1.00 fitness: 929.19 spacedDyad: yGTGGGAA motifConsensus: AkGGwGAr 0.50 fitness: 2744.13 spacedDyad: yGTGGGAA motifConsensus: TTTCTkwA 0.10 fitness: 3745.37 GADEM cycle[ 9] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: rsAGTGAG 0.60 fitness: 748.08 spacedDyad: yGTGGGAA motifConsensus: TkTGwGAr 0.30 fitness: 3743.09 spacedDyad: yGTGGGAA motifConsensus: TTTrTkAA 0.10 fitness: 3864.37 GADEM cycle[ 10] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: AAAATAAw 1.00 fitness: 2242.20 GADEM cycle[ 11] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CArGwGwT 0.50 fitness: 783.09 spacedDyad: yGTGGGAA motifConsensus: AAwGTrAw 0.40 fitness: 3189.27 GADEM cycle[ 12] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: mCAGGAAr 0.70 fitness: 555.70 spacedDyad: yGTGGGAA motifConsensus: sAGGGAAr 0.30 fitness: 2555.32 spacedDyad: yGTGGGAA motifConsensus: yATGTGAA 0.10 fitness: 4216.06 GADEM cycle[ 13] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: yCTGGArr 0.90 fitness: 2745.77 spacedDyad: yGTGGGAA motifConsensus: TGkGGswG 0.50 fitness: 2760.47 GADEM cycle[ 14] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: CwwGrAAA 0.30 fitness: 2655.60 GADEM cycle[ 15] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: vAAGGmAG 1.00 fitness: 2828.79 spacedDyad: yGTGGGAA motifConsensus: TTTGGrrT 0.20 fitness: 3368.61 spacedDyad: yGTGGGAA motifConsensus: yCTGGGCT 0.10 fitness: 4055.44 GADEM cycle[ 16] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: rGTGGCws 0.80 fitness: 2575.82 spacedDyad: yGTGGGAA motifConsensus: ACAGArAG 1.00 fitness: 3621.22 GADEM cycle[ 17] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: rmTGArAT 1.00 fitness: 2941.59 spacedDyad: yGTGGGAA motifConsensus: AsTGGsAG 0.20 fitness: 3224.73 spacedDyad: yGTGGGAA motifConsensus: AmwGrGAG 0.70 fitness: 3508.73 GADEM cycle[ 18] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: nTTTTAAT 0.50 fitness: 3008.72 spacedDyad: yGTGGGAA motifConsensus: CCTGkrrT 0.30 fitness: 3071.58 spacedDyad: yGTGGGAA motifConsensus: GATGGGGT 0.20 fitness: 3527.31 GADEM cycle[ 19] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: wTTTTAAk 0.60 fitness: 2431.45 spacedDyad: yGTGGGAA motifConsensus: CTkkGsCT 0.20 fitness: 3870.61 GADEM cycle[ 20] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: mTTyTGAw 0.40 fitness: 3086.88 spacedDyad: yGTGGGAA motifConsensus: rTwGrAAA 0.90 fitness: 3089.77 spacedDyad: yGTGGGAA motifConsensus: CTTGrrrT 0.30 fitness: 3746.72 spacedDyad: yGTGGGAA motifConsensus: sATGGGAG 0.10 fitness: 4436.80 GADEM cycle[ 21] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TyTsTGyT 0.60 fitness: 3340.43 spacedDyad: yGTGGGAA motifConsensus: TGTGksCw 0.30 fitness: 3938.04 GADEM cycle[ 22] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: TsTkTyTT 0.70 fitness: 3026.39 spacedDyad: yGTGGGAA motifConsensus: yCTGkCTy 0.20 fitness: 3090.98 spacedDyad: yGTGGGAA motifConsensus: GCwGTGrT 0.30 fitness: 3273.31 spacedDyad: yGTGGGAA motifConsensus: TAkGrGAr 0.10 fitness: 3354.05 spacedDyad: yGTGGGAA motifConsensus: TGwGTCwk 1.00 fitness: 3797.66 GADEM cycle[ 23] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: AGArwGAA 1.00 fitness: 1460.77 spacedDyad: yGTGGGAA motifConsensus: sCTswGAA 0.20 fitness: 3587.30 GADEM cycle[ 24] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: ATrTTwAA 0.90 fitness: 1715.27 spacedDyad: yGTGGGAA motifConsensus: rkAGArAA 0.60 fitness: 2892.91 spacedDyad: yGTGGGAA motifConsensus: mTTGwGAA 0.20 fitness: 3329.57 spacedDyad: yGTGGGAA motifConsensus: ATAAwAAA 0.80 fitness: 3764.84 GADEM cycle[ 25] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TGTGGmAT 0.50 fitness: 2616.24 spacedDyad: yGTGGGAA motifConsensus: GGGGGAAA 0.10 fitness: 3769.90 GADEM cycle[ 26] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: yATTTTAT 0.70 fitness: 2885.27 spacedDyad: yGTGGGAA motifConsensus: CATkTGmy 0.30 fitness: 3247.68 spacedDyad: yGTGGGAA motifConsensus: TGTGTGmC 0.10 fitness: 4272.69 GADEM cycle[ 27] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: TTTAGTAG 1.00 fitness: 1631.95 spacedDyad: yGTGGGAA motifConsensus: TyTTTGyT 0.50 fitness: 3265.59 spacedDyad: yGTGGGAA motifConsensus: rGTkTGmA 0.10 fitness: 3303.55 spacedDyad: yGTGGGAA motifConsensus: TGTkkGkT 0.20 fitness: 3635.28 GADEM cycle[ 28] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: yTTGkCTk 0.50 fitness: 2779.39 spacedDyad: yGTGGGAA motifConsensus: TCTGGGwy 0.20 fitness: 3046.02 spacedDyad: yGTGGGAA motifConsensus: yyTGGCTG 1.00 fitness: 3683.18 GADEM cycle[ 29] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: TTTrkAAG 0.90 fitness: 1494.81 spacedDyad: yGTGGGAA motifConsensus: CAGkGmCy 0.30 fitness: 3065.00 spacedDyad: yGTGGGAA motifConsensus: TGwGGGmy 0.10 fitness: 3229.95 spacedDyad: yGTGGGAA motifConsensus: TTTGTCwk 0.50 fitness: 3490.15 GADEM cycle[ 30] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: CTwATTTT 0.30 fitness: 3360.69 spacedDyad: yGTGGGAA motifConsensus: CCTGGCyA 0.20 fitness: 3432.94 spacedDyad: yGTGGGAA motifConsensus: CCTGGGCA 0.10 fitness: 4076.08 GADEM cycle[ 31] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: wATTTTTw 1.00 fitness: 2700.13 spacedDyad: yGTGGGAA motifConsensus: TATkTATT 0.30 fitness: 2732.84 spacedDyad: yGTGGGAA motifConsensus: CAwGGCmw 0.20 fitness: 3417.36 spacedDyad: yGTGGGAA motifConsensus: CATGrGsw 0.10 fitness: 3785.42 GADEM cycle[ 32] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: TTTsTwAT 0.30 fitness: 3262.46 spacedDyad: yGTGGGAA motifConsensus: swGsTGAG 0.20 fitness: 3670.24 spacedDyad: yGTGGGAA motifConsensus: CCTGGGTk 0.10 fitness: 3914.55 GADEM cycle[ 33] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: mwTGrAAG 0.50 fitness: 2776.81 spacedDyad: yGTGGGAA motifConsensus: sAGsTCAG 0.30 fitness: 3340.91 spacedDyad: yGTGGGAA motifConsensus: CTkGGTGn 0.10 fitness: 3609.09 spacedDyad: yGTGGGAA motifConsensus: CTTkGAAG 0.90 fitness: 3808.79 spacedDyad: yGTGGGAA motifConsensus: AATGmmwG 0.40 fitness: 3987.45 GADEM cycle[ 34] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: wArATATT 0.40 fitness: 2690.90 spacedDyad: yGTGGGAA motifConsensus: AAAAGCAG 0.70 fitness: 2956.35 spacedDyad: yGTGGGAA motifConsensus: GwTGGrAT 0.20 fitness: 3084.78 spacedDyad: yGTGGGAA motifConsensus: GGCGGGGC 0.10 fitness: 3483.46 GADEM cycle[ 35] generation[ 1] number of unique motif(s): 6 spacedDyad: yGTGGGAA motifConsensus: wGTTkCwG 0.80 fitness: 3085.01 spacedDyad: yGTGGGAA motifConsensus: TGTGTmTr 1.00 fitness: 3142.33 spacedDyad: yGTGGGAA motifConsensus: TCAGGArG 0.40 fitness: 3351.63 spacedDyad: yGTGGGAA motifConsensus: CATTTTkG 0.30 fitness: 3774.37 spacedDyad: yGTGGGAA motifConsensus: CTGCwGCy 0.20 fitness: 3785.57 spacedDyad: yGTGGGAA motifConsensus: GCTGGGrC 0.10 fitness: 3799.44 GADEM cycle[ 36] generation[ 1] number of unique motif(s): 6 spacedDyad: yGTGGGAA motifConsensus: ATTmTTAT 0.30 fitness: 2712.42 spacedDyad: yGTGGGAA motifConsensus: CrTGGTGG 0.10 fitness: 3201.57 spacedDyad: yGTGGGAA motifConsensus: AATGrAAG 0.50 fitness: 3243.11 spacedDyad: yGTGGGAA motifConsensus: CTTsTksT 0.20 fitness: 3518.97 spacedDyad: yGTGGGAA motifConsensus: AArGAGAG 0.40 fitness: 3523.27 spacedDyad: yGTGGGAA motifConsensus: ArAAGAAG 0.80 fitness: 3620.03 GADEM cycle[ 37] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: CAGkkTTT 0.30 fitness: 3132.61 spacedDyad: yGTGGGAA motifConsensus: TyTGksCA 0.50 fitness: 3214.09 spacedDyad: yGTGGGAA motifConsensus: CAArwyCA 0.40 fitness: 3350.80 spacedDyad: yGTGGGAA motifConsensus: AGTGGrkk 0.10 fitness: 3378.32 spacedDyad: yGTGGGAA motifConsensus: CmTsTkTT 0.20 fitness: 3405.97 GADEM cycle[ 38] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: TAArGCAr 0.50 fitness: 2291.58 spacedDyad: yGTGGGAA motifConsensus: CAkATAAw 0.30 fitness: 2914.42 spacedDyad: yGTGGGAA motifConsensus: CsyGGGGG 0.10 fitness: 3036.77 spacedDyad: yGTGGGAA motifConsensus: yTGrGGAG 0.20 fitness: 3279.92 spacedDyad: yGTGGGAA motifConsensus: TwAGkAAA 0.40 fitness: 3290.05 GADEM cycle[ 39] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: CGTGGGrw 0.10 fitness: 2409.67 spacedDyad: yGTGGGAA motifConsensus: CyTGTGAs 0.20 fitness: 2591.47 spacedDyad: yGTGGGAA motifConsensus: AswGGCAT 1.00 fitness: 2935.71 spacedDyad: yGTGGGAA motifConsensus: CCwGAAAr 0.50 fitness: 3394.29 spacedDyad: yGTGGGAA motifConsensus: CCAGTCws 0.60 fitness: 3620.07