processor ID: 12042 ========================================================================== |------------------------------------------------------------------| | | | *** 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/a/HS1235-p1em6_3642-selfUnion-pm400bp.hg18.20100718.fa.3stage_dm_w4.fa.pwmCSL-MEME-m1.mx.weight0.de_novo -minN 500 -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: 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 18 05:50:27 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 0.90 fitness: 420.48 spacedDyad: yGTGGGAA motifConsensus: TTTrTArA 0.30 fitness: 1018.17 spacedDyad: yGTGGGAA motifConsensus: TATkTGAA 0.20 fitness: 1307.40 GADEM cycle[ 4] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TyTswGAA 0.90 fitness: 349.90 spacedDyad: yGTGGGAA motifConsensus: TTTGGGAr 0.30 fitness: 1213.88 GADEM cycle[ 5] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: AAAAAGAA 0.10 fitness: 565.78 spacedDyad: yGTGGGAA motifConsensus: AATkAAAA 1.00 fitness: 1192.51 GADEM cycle[ 6] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: rGArrAAA 1.00 fitness: 616.24 spacedDyad: yGTGGGAA motifConsensus: AAAGkGAA 0.30 fitness: 1926.67 GADEM cycle[ 7] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: AATACAAA 1.00 fitness: 916.30 spacedDyad: yGTGGGAA motifConsensus: wCTwAAAA 0.60 fitness: 1140.44 spacedDyad: yGTGGGAA motifConsensus: wGkGrAAA 0.30 fitness: 1329.38 spacedDyad: yGTGGGAA motifConsensus: ArTGAGAA 0.20 fitness: 1542.86 GADEM cycle[ 8] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CCTGkAAT 1.00 fitness: 799.11 spacedDyad: yGTGGGAA motifConsensus: ymAGGAAA 0.40 fitness: 983.88 GADEM cycle[ 9] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: sCTGGsmw 0.40 fitness: -689.84 spacedDyad: yGTGGGAA motifConsensus: kCTkTGAr 0.70 fitness: 781.62 spacedDyad: yGTGGGAA motifConsensus: mATTTrAA 0.80 fitness: 1190.31 GADEM cycle[ 10] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: TTTkTGAT 0.90 fitness: 1121.27 spacedDyad: yGTGGGAA motifConsensus: krArAGAA 0.50 fitness: 1127.06 spacedDyad: yGTGGGAA motifConsensus: sAkTTGAA 0.60 fitness: 1359.92 spacedDyad: yGTGGGAA motifConsensus: TrTGGGAA 0.10 fitness: 1624.94 GADEM cycle[ 11] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: CwTGmAAA 0.40 fitness: 1002.48 spacedDyad: yGTGGGAA motifConsensus: AATGTrAA 0.50 fitness: 1069.09 spacedDyad: yGTGGGAA motifConsensus: AATATTTw 0.90 fitness: 1283.64 GADEM cycle[ 12] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: kGAGrCAG 0.80 fitness: -688.02 spacedDyad: yGTGGGAA motifConsensus: CArrAGmA 0.50 fitness: 358.03 spacedDyad: yGTGGGAA motifConsensus: CTTGrGAA 0.10 fitness: 2014.33 GADEM cycle[ 13] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: rGTGGmAk 0.70 fitness: 833.92 spacedDyad: yGTGGGAA motifConsensus: TrTkGAAT 0.80 fitness: 1092.05 spacedDyad: yGTGGGAA motifConsensus: TrTTTATT 1.00 fitness: 1102.19 spacedDyad: yGTGGGAA motifConsensus: GGwGGGrG 0.20 fitness: 1599.35 GADEM cycle[ 14] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: ATTwTTTT 1.00 fitness: 805.08 spacedDyad: yGTGGGAA motifConsensus: dkTTTGAA 0.20 fitness: 1247.98 GADEM cycle[ 15] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: AATkTTTT 0.50 fitness: 1005.32 spacedDyad: yGTGGGAA motifConsensus: TGTGTGyA 0.10 fitness: 1351.24 GADEM cycle[ 16] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: mCArAAAT 0.60 fitness: 836.07 spacedDyad: yGTGGGAA motifConsensus: AATATAAT 0.10 fitness: 1038.21 spacedDyad: yGTGGGAA motifConsensus: CAAGwGAT 0.30 fitness: 1095.82 spacedDyad: yGTGGGAA motifConsensus: AAAAwkAG 1.00 fitness: 1385.84 GADEM cycle[ 17] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: CwTGrAAk 0.60 fitness: 1070.47 spacedDyad: yGTGGGAA motifConsensus: CATTTGwT 0.40 fitness: 1182.22 spacedDyad: yGTGGGAA motifConsensus: AATGwGAT 0.10 fitness: 1420.77 GADEM cycle[ 18] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: rArkkCAG 0.60 fitness: 708.38 spacedDyad: yGTGGGAA motifConsensus: GAGswCAG 0.50 fitness: 1304.94 spacedDyad: yGTGGGAA motifConsensus: ATGswGAA 0.40 fitness: 1363.49 spacedDyad: yGTGGGAA motifConsensus: wTTTGswG 1.00 fitness: 1478.22 GADEM cycle[ 19] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: yATTTTAG 0.60 fitness: 982.36 spacedDyad: yGTGGGAA motifConsensus: GATGwGAA 0.30 fitness: 1058.87 spacedDyad: yGTGGGAA motifConsensus: TsTTTCTG 1.00 fitness: 1314.22 GADEM cycle[ 20] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: ATTTTGmT 0.10 fitness: 1164.06 spacedDyad: yGTGGGAA motifConsensus: AyTGrAAT 0.20 fitness: 1176.71 spacedDyad: yGTGGGAA motifConsensus: TTTGGmAG 0.80 fitness: 1407.05 GADEM cycle[ 21] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: AATGwmwG 0.50 fitness: 1252.11 spacedDyad: yGTGGGAA motifConsensus: mAwGrAAG 0.40 fitness: 1335.07 spacedDyad: yGTGGGAA motifConsensus: yTTkTCTG 0.80 fitness: 1335.73 spacedDyad: yGTGGGAA motifConsensus: CTTGTTTT 0.60 fitness: 1507.42 spacedDyad: yGTGGGAA motifConsensus: ATTCTGAk 0.10 fitness: 1510.71 GADEM cycle[ 22] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: TGwkTCAT 0.90 fitness: 1121.15 spacedDyad: yGTGGGAA motifConsensus: GmwGGmAk 0.40 fitness: 1285.96 spacedDyad: yGTGGGAA motifConsensus: GTkGwGAr 0.10 fitness: 1340.33 spacedDyad: yGTGGGAA motifConsensus: GwTGGsAr 0.30 fitness: 1469.03 spacedDyad: yGTGGGAA motifConsensus: sTTkGCTT 0.70 fitness: 1605.82 GADEM cycle[ 23] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: wGwGTAAA 1.00 fitness: 1032.65 spacedDyad: yGTGGGAA motifConsensus: TGTkTTwT 0.40 fitness: 1135.29 spacedDyad: yGTGGGAA motifConsensus: wGAsTsAG 0.30 fitness: 1362.40 spacedDyad: yGTGGGAA motifConsensus: AGTTTsAG 0.70 fitness: 1425.30 GADEM cycle[ 24] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TsTGTyTT 0.80 fitness: 1045.34 spacedDyad: yGTGGGAA motifConsensus: CATATTTA 0.20 fitness: 1101.81 GADEM cycle[ 25] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: TGyTTTAT 0.90 fitness: 919.45 spacedDyad: yGTGGGAA motifConsensus: CATkTTwT 0.50 fitness: 1061.60 spacedDyad: yGTGGGAA motifConsensus: TCTGTkTw 0.30 fitness: 1102.13 GADEM cycle[ 26] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: ymAGTkAA 0.30 fitness: 1075.62 spacedDyad: yGTGGGAA motifConsensus: yATTTTAT 0.60 fitness: 1167.68 spacedDyad: yGTGGGAA motifConsensus: CATGTkmw 0.10 fitness: 1371.12 GADEM cycle[ 27] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CTTrGAAA 0.20 fitness: 1229.42 spacedDyad: yGTGGGAA motifConsensus: TTTGkCAA 0.40 fitness: 1246.54 GADEM cycle[ 28] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TrkGTGAy 0.30 fitness: 1099.32 spacedDyad: yGTGGGAA motifConsensus: ksTGTGrT 0.50 fitness: 1381.68 GADEM cycle[ 29] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: AywGAGmA 0.20 fitness: 948.30 spacedDyad: yGTGGGAA motifConsensus: AAwrGCAw 0.30 fitness: 1175.53 spacedDyad: yGTGGGAA motifConsensus: wTkTGGwT 0.40 fitness: 1222.29 spacedDyad: yGTGGGAA motifConsensus: AGAGrGAA 0.10 fitness: 1704.18 GADEM cycle[ 30] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: mTGArGAT 0.30 fitness: 1014.73 spacedDyad: yGTGGGAA motifConsensus: TTkrGGwT 0.40 fitness: 1188.97 spacedDyad: yGTGGGAA motifConsensus: ACTGTkyT 0.10 fitness: 1292.31 spacedDyad: yGTGGGAA motifConsensus: GTGAGCCA 0.20 fitness: 1453.34 GADEM cycle[ 31] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: ACTkTTAG 0.30 fitness: 1108.52 spacedDyad: yGTGGGAA motifConsensus: AGTGTGnw 0.10 fitness: 1508.13 GADEM cycle[ 32] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: wCTkGmAG 0.50 fitness: 854.16 spacedDyad: yGTGGGAA motifConsensus: yCwGGmwG 0.30 fitness: 872.91 spacedDyad: yGTGGGAA motifConsensus: TAATkCAk 0.80 fitness: 1053.78 spacedDyad: yGTGGGAA motifConsensus: CCTGGrAG 0.10 fitness: 2103.64 GADEM cycle[ 33] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: ATTrGsAr 0.10 fitness: 1213.37 spacedDyad: yGTGGGAA motifConsensus: TArAGAAG 0.60 fitness: 1232.55 spacedDyad: yGTGGGAA motifConsensus: CArrGCwG 0.40 fitness: 1323.35 GADEM cycle[ 34] generation[ 1] number of unique motif(s): 0 finished: Sun Jul 18 18:35:22 2010 approximated processor time in seconds: 45895.000000