processor ID: 13381 ========================================================================== |------------------------------------------------------------------| | | | *** Running a seeded analysis *** | | | |------------------------------------------------------------------| command line: /home/grobertson/Fi/Code/20101203/GADEM_v1.3/bin/gadem -fseq /projects/remc_bigdata/Karsan/motifs/20101227/FA/KD-DE_133-self-union-TSSrgns.hg18.20101227.fa.3rd_stage_dmasker_w4.fa -fout /projects/remc_bigdata/Karsan/motifs/20101227/KD-DE/seed_CSL_m1/a/KD-DE_133-self-union-TSSrgns.hg18.20101227.fa.3rd_stage_dmasker_w4.fa.pwmCSL-MEME-m1.mx.fEM0.5.minN40.maxgap10.pgf0.pv0.0002.wt0.de_novo -em 40 -ev 500 -fEM 0.5 -fpwm0 /projects/remc_bigdata/Karsan/motifs/PWMs/CSL-MEME-m1.mx -minN 40 -pv 0.0002 -posWt 0 -extTrim 1 -pgf 0 -fbm /home/grobertson/Fi/Code/20101203/GADEM_v1.3/KmerFreq/hg18_kmer_1to9_freq.txt -bOrder 3 -verbose 1 maximal buffer length: 15000 maximal number of sequences set: 44000 maximal number of bases per seq read: 20000 maximal number of sites in a motif: 150000 input (ChIP) sequence file: /projects/remc_bigdata/Karsan/motifs/20101227/FA/KD-DE_133-self-union-TSSrgns.hg18.20101227.fa.3rd_stage_dmasker_w4.fa number of sequences in input file: 133 average sequence length: 3099 total number of nucleotides: 412278 max number of generations: 1 population size: 10 use a user-specified pwm as the seed /projects/remc_bigdata/Karsan/motifs/PWMs/CSL-MEME-m1.mx fraction (number) input sequences subject to EM 1.00 (133) scale factor for converting (double)pwm to (int)pwm 200 number of EM steps: 40 EM convergence criterion: 1.000000e-04 run EM on the starting pwm /projects/remc_bigdata/Karsan/motifs/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: 40 base extension and trimming? yes sliding window for comparing pwm similarity: 6 PWM similarity cutoff: 0.300 log(E-value) cutoff: 500.00 number of adjacent bases included in binding site output: 10 job started: Mon Dec 27 20:21:16 2010 ========================================================================= GADEM cycle[ 1] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: GGAGGGAG 0.70 fitness: 17.20 GADEM cycle[ 2] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: GGwGGGGA 0.50 fitness: 44.01 GADEM cycle[ 3] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: rGwGGGAA 1.00 fitness: 128.07 GADEM cycle[ 4] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: yTTGGGAG 1.00 fitness: 175.69 GADEM cycle[ 5] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CTGGGGrA 1.00 fitness: 143.98 spacedDyad: yGTGGGAA motifConsensus: TkTGGrrA 0.60 fitness: 195.65 GADEM cycle[ 6] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CAGGAGAr 1.00 fitness: 139.55 spacedDyad: yGTGGGAA motifConsensus: CCTGGGmm 0.70 fitness: 142.36 GADEM cycle[ 7] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: AAAGAAAA 1.00 fitness: -39.93 spacedDyad: yGTGGGAA motifConsensus: CwTGGArA 0.10 fitness: 230.12 GADEM cycle[ 8] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: AGAGGrAG 0.90 fitness: 114.41 GADEM cycle[ 9] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: TGGGGsTG 1.00 fitness: 190.22 spacedDyad: yGTGGGAA motifConsensus: kGTGGGrG 0.70 fitness: 212.06 spacedDyad: yGTGGGAA motifConsensus: CGGGGGCG 0.10 fitness: 265.88 GADEM cycle[ 10] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: AGGswGAG 0.90 fitness: 146.20 spacedDyad: yGTGGGAA motifConsensus: CGCGGGGG 0.20 fitness: 246.03 spacedDyad: yGTGGGAA motifConsensus: AGkGAGAA 0.60 fitness: 263.62 GADEM cycle[ 11] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: GrGsTsAG 0.80 fitness: 172.87 spacedDyad: yGTGGGAA motifConsensus: rrwGTGAr 0.40 fitness: 213.85 spacedDyad: yGTGGGAA motifConsensus: CGTGGGAr 0.20 fitness: 215.15 GADEM cycle[ 12] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: GCTGGGAT 1.00 fitness: 88.22 spacedDyad: yGTGGGAA motifConsensus: TTTTTAAA 0.80 fitness: 193.36 GADEM cycle[ 13] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: yyTCwGAG 0.70 fitness: 189.59 spacedDyad: yGTGGGAA motifConsensus: rAGGrGAG 0.90 fitness: 217.00 GADEM cycle[ 14] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: GATGGGGr 1.00 fitness: 232.11 spacedDyad: yGTGGGAA motifConsensus: mTGGwGAA 0.70 fitness: 245.88 spacedDyad: yGTGGGAA motifConsensus: TTTCwGAA 0.60 fitness: 268.30 GADEM cycle[ 15] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: wmTGnAAA 0.60 fitness: 213.27 spacedDyad: yGTGGGAA motifConsensus: AATkrrAr 1.00 fitness: 229.54 spacedDyad: yGTGGGAA motifConsensus: AAkrGAAr 0.80 fitness: 235.51 GADEM cycle[ 16] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CCTGGsCT 1.00 fitness: 150.56 spacedDyad: yGTGGGAA motifConsensus: CAGskGCm 0.30 fitness: 199.84 GADEM cycle[ 17] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TyTGTryT 0.70 fitness: 198.15 spacedDyad: yGTGGGAA motifConsensus: CCTGTGCy 0.40 fitness: 273.34 GADEM cycle[ 18] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: CAkGTGws 0.70 fitness: 225.23 GADEM cycle[ 19] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: TkTGGrsT 0.80 fitness: 187.86 spacedDyad: yGTGGGAA motifConsensus: GCTGGAGk 1.00 fitness: 189.51 spacedDyad: yGTGGGAA motifConsensus: TGTGkGCy 0.60 fitness: 232.75 GADEM cycle[ 20] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: sCAGGmAG 0.90 fitness: 187.80 spacedDyad: yGTGGGAA motifConsensus: TGTTTmTT 0.60 fitness: 199.54 spacedDyad: yGTGGGAA motifConsensus: TGkGTGAC 0.40 fitness: 252.23 GADEM cycle[ 21] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CATGGsAG 0.10 fitness: 229.61 spacedDyad: yGTGGGAA motifConsensus: ywwGGAAG 0.80 fitness: 230.87 GADEM cycle[ 22] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: GGTGGmrG 0.80 fitness: 198.78 spacedDyad: yGTGGGAA motifConsensus: ACTGkGAT 0.30 fitness: 279.30 spacedDyad: yGTGGGAA motifConsensus: AAGGAGAT 0.20 fitness: 291.83 GADEM cycle[ 23] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: GkTkGrrT 0.90 fitness: 210.94 spacedDyad: yGTGGGAA motifConsensus: GGwGGArm 1.00 fitness: 227.96 spacedDyad: yGTGGGAA motifConsensus: AATGTGmT 0.20 fitness: 259.95 spacedDyad: yGTGGGAA motifConsensus: AwTTTAAT 0.30 fitness: 302.31 GADEM cycle[ 24] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: GTkGkGAG 0.70 fitness: 194.64 spacedDyad: yGTGGGAA motifConsensus: CCTGGCCA 0.40 fitness: 237.08 spacedDyad: yGTGGGAA motifConsensus: TCTGTGAA 0.10 fitness: 274.52 GADEM cycle[ 25] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: CTGGGsCy 1.00 fitness: 211.95 GADEM cycle[ 26] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CCTGkCTC 0.90 fitness: 194.45 spacedDyad: yGTGGGAA motifConsensus: CAGGGyCh 0.10 fitness: 221.23 GADEM cycle[ 27] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: CTTGksmC 0.40 fitness: 207.73 spacedDyad: yGTGGGAA motifConsensus: CyGGGCAs 1.00 fitness: 230.00 spacedDyad: yGTGGGAA motifConsensus: mTTTTsAA 0.50 fitness: 241.97 spacedDyad: yGTGGGAA motifConsensus: CTTTGCCT 0.10 fitness: 293.60 GADEM cycle[ 28] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: yTkGkCCA 0.70 fitness: 214.81 spacedDyad: yGTGGGAA motifConsensus: ryTGAGAA 0.60 fitness: 220.42 spacedDyad: yGTGGGAA motifConsensus: AGTGGCAs 0.90 fitness: 223.68 spacedDyad: yGTGGGAA motifConsensus: CTGswGCT 0.20 fitness: 240.17 spacedDyad: yGTGGGAA motifConsensus: AGGAGGCT 0.10 fitness: 244.88 GADEM cycle[ 29] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: CykGGGkT 0.60 fitness: 194.23 spacedDyad: yGTGGGAA motifConsensus: CmAGGGmT 0.90 fitness: 232.49 spacedDyad: yGTGGGAA motifConsensus: CTGGGGAT 0.20 fitness: 271.24 GADEM cycle[ 30] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: TAGGrrAr 0.10 fitness: 195.58 spacedDyad: yGTGGGAA motifConsensus: wsAGGCTG 1.00 fitness: 198.67 spacedDyad: yGTGGGAA motifConsensus: ACAGGCry 0.60 fitness: 213.34 spacedDyad: yGTGGGAA motifConsensus: AGAGrGrC 0.40 fitness: 221.51 spacedDyad: yGTGGGAA motifConsensus: TGrGTCAG 0.20 fitness: 247.56 GADEM cycle[ 31] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: CTTGAACy 0.30 fitness: 172.14 spacedDyad: yGTGGGAA motifConsensus: wGwGGAkG 0.80 fitness: 188.84 spacedDyad: yGTGGGAA motifConsensus: TGGGTGsT 0.20 fitness: 230.03 spacedDyad: yGTGGGAA motifConsensus: TGAGACCA 0.10 fitness: 276.41 GADEM cycle[ 32] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: ksTGGCyT 0.60 fitness: 189.93 spacedDyad: yGTGGGAA motifConsensus: GGkGGGCT 0.40 fitness: 203.24 spacedDyad: yGTGGGAA motifConsensus: yTTGkTTT 0.30 fitness: 235.45 spacedDyad: yGTGGGAA motifConsensus: TGTGTGCA 0.10 fitness: 240.32 GADEM cycle[ 33] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: wAAkrAAT 0.80 fitness: 212.09 spacedDyad: yGTGGGAA motifConsensus: CywGrAAT 0.90 fitness: 219.69 spacedDyad: yGTGGGAA motifConsensus: TGAGGAAA 0.10 fitness: 220.04 spacedDyad: yGTGGGAA motifConsensus: CAGsTAAT 0.20 fitness: 247.63 GADEM cycle[ 34] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: AGGGGGnm 0.30 fitness: 154.39 spacedDyad: yGTGGGAA motifConsensus: TTTGkGrC 0.50 fitness: 174.59 spacedDyad: yGTGGGAA motifConsensus: TyTGGsAC 0.60 fitness: 197.44 spacedDyad: yGTGGGAA motifConsensus: mkGsTGAT 0.20 fitness: 211.24 spacedDyad: yGTGGGAA motifConsensus: CGGGGCGs 0.10 fitness: 223.29 GADEM cycle[ 35] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: ArTGkCmA 0.60 fitness: 164.88 spacedDyad: yGTGGGAA motifConsensus: TATGGGAG 0.10 fitness: 185.96 spacedDyad: yGTGGGAA motifConsensus: nCTGTCwk 1.00 fitness: 216.41 spacedDyad: yGTGGGAA motifConsensus: AGTGwsCT 0.30 fitness: 217.95 GADEM cycle[ 36] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: mGTGGGGA 0.20 fitness: 151.77 spacedDyad: yGTGGGAA motifConsensus: sTTGGGCw 0.50 fitness: 190.68 spacedDyad: yGTGGGAA motifConsensus: ATTTTTrT 1.00 fitness: 208.25 GADEM cycle[ 37] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: sTTGTmAT 0.60 fitness: 169.29 spacedDyad: yGTGGGAA motifConsensus: GTTrksAA 0.50 fitness: 183.71 spacedDyad: yGTGGGAA motifConsensus: GTTGGkwA 0.40 fitness: 184.94 spacedDyad: yGTGGGAA motifConsensus: TGAGTCCT 0.10 fitness: 220.46 spacedDyad: yGTGGGAA motifConsensus: CTTTTGAk 0.20 fitness: 258.15 GADEM cycle[ 38] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: ArTGkwwT 1.00 fitness: 174.68 spacedDyad: yGTGGGAA motifConsensus: TGTTTyAT 0.20 fitness: 232.29