processor ID: 22691 ========================================================================== |------------------------------------------------------------------| | | | *** Running a seeded analysis *** | | | |------------------------------------------------------------------| command line: /home/grobertson/Fi/Code/20090926_v1.3/Fi_v1.3/bin/fi -fseq /projects/remc_bigdata/Karsan/HS1235_ctl/compare/FA_NEW/HS1235-p1em6_3642-selfUnion-pm400bp.hg18.20100718.fa.3stage_dm_w4.fa -fout /projects/remc_bigdata/Karsan/HS1235_ctl/compare/seed_RBPJ_MEME-m1/b/HS1235-p1em6_3642-selfUnion-pm400bp.hg18.20100718.fa.3stage_dm_w4.fa.pwmCSL-MEME-m1.mx.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/HS1235_ctl/compare/FA_NEW/HS1235-p1em6_3642-selfUnion-pm400bp.hg18.20100718.fa.3stage_dm_w4.fa number of sequences in input file: 3642 average sequence length: 839 total number of nucleotides: 3057409 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 (3642) 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: Tue Jul 20 10:05:12 2010 ========================================================================= GADEM cycle[ 1] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: AAwGGAAw 1.00 fitness: -750.76 spacedDyad: yGTGGGAA motifConsensus: TTTTkAAA 0.60 fitness: 305.22 GADEM cycle[ 2] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: TTTGGAAA 0.10 fitness: 844.61 GADEM cycle[ 3] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: AAAkAAAA 0.80 fitness: 323.46 spacedDyad: yGTGGGAA motifConsensus: TTTrTArA 0.30 fitness: 1018.17 spacedDyad: yGTGGGAA motifConsensus: TATkTGAA 0.20 fitness: 1305.96 GADEM cycle[ 4] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TyTswGAA 0.70 fitness: 347.64 spacedDyad: yGTGGGAA motifConsensus: TTTGGGAr 0.30 fitness: 1138.06 GADEM cycle[ 5] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: AGArrAAA 0.50 fitness: 802.85 spacedDyad: yGTGGGAA motifConsensus: AAAAAkAA 0.30 fitness: 1377.27 spacedDyad: yGTGGGAA motifConsensus: AAAGAGAA 0.10 fitness: 1885.12 GADEM cycle[ 6] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: AGkrrAAA 0.40 fitness: 975.01 spacedDyad: yGTGGGAA motifConsensus: AAAGGGAA 0.20 fitness: 1996.29 GADEM cycle[ 7] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: TAwGAAAA 0.90 fitness: 1041.40 GADEM cycle[ 8] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TswrGAAA 0.90 fitness: 1042.46 spacedDyad: yGTGGGAA motifConsensus: TmTTAAAA 1.00 fitness: 1475.90 GADEM cycle[ 9] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: GCTGGGAT 0.30 fitness: 691.44 spacedDyad: yGTGGGAA motifConsensus: AAwrCAAA 1.00 fitness: 787.52 spacedDyad: yGTGGGAA motifConsensus: AmTGwGAA 0.60 fitness: 1268.74 spacedDyad: yGTGGGAA motifConsensus: kswGGGAA 0.20 fitness: 1269.59 GADEM cycle[ 10] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TTTsTGwT 0.80 fitness: 552.27 spacedDyad: yGTGGGAA motifConsensus: CwTGrAAA 0.20 fitness: 1218.03 GADEM cycle[ 11] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: AGrmAGAA 0.70 fitness: 840.85 spacedDyad: yGTGGGAA motifConsensus: ATGGwGAA 0.40 fitness: 1168.64 spacedDyad: yGTGGGAA motifConsensus: ATTTkGAG 0.90 fitness: 1366.27 GADEM cycle[ 12] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: CCTGGsCA 0.20 fitness: 613.34 spacedDyad: yGTGGGAA motifConsensus: wswGGAAG 0.90 fitness: 1186.02 spacedDyad: yGTGGGAA motifConsensus: AAAkAAAk 0.50 fitness: 1220.02 spacedDyad: yGTGGGAA motifConsensus: CwkGAGAA 0.40 fitness: 1281.56 GADEM cycle[ 13] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: rswGTGAG 0.70 fitness: 360.70 spacedDyad: yGTGGGAA motifConsensus: GGAGGsAG 0.30 fitness: 906.43 GADEM cycle[ 14] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: AGAAGGAA 0.10 fitness: 1993.98 GADEM cycle[ 15] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: AGkGGGAA 0.10 fitness: 1783.60 GADEM cycle[ 16] generation[ 1] number of unique motif(s): 0 finished: Tue Jul 20 15:43:57 2010 approximated processor time in seconds: 20325.000000