processor ID: 26751 ========================================================================== |------------------------------------------------------------------| | | | *** 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_Ebox_M01034/a/HS1235-p1em6_3642-selfUnion-pm400bp.hg18.20100718.fa.3stage_dm_w4.fa.pwmEbox_M01034.mx.weight0.de_novo -minN 500 -ev 5000 -pv 0.0002 -fpwm0 /home/grobertson/Fi/PWMs/Ebox_M01034.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/Ebox_M01034.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/Ebox_M01034.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 05:53:42 2010 ========================================================================= GADEM cycle[ 1] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: TTTnywTTTT 1.00 fitness: -675.24 spacedDyad: nCACsTGnyn motifConsensus: yCTCCTGCCT 0.10 fitness: 552.43 GADEM cycle[ 2] generation[ 1] number of unique motif(s): 1 spacedDyad: nCACsTGnyn motifConsensus: wwwTTTwAAA 1.00 fitness: 1366.63 GADEM cycle[ 3] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: wwwwTTmTTT 0.90 fitness: 1275.45 spacedDyad: nCACsTGnyn motifConsensus: rAAAATrTTT 0.20 fitness: 2181.00 GADEM cycle[ 4] generation[ 1] number of unique motif(s): 1 spacedDyad: nCACsTGnyn motifConsensus: wAAAAwTAyw 0.30 fitness: 1428.36 GADEM cycle[ 5] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: TCTTTTTsTw 1.00 fitness: 1153.27 spacedDyad: nCACsTGnyn motifConsensus: TyrAACTCCT 0.10 fitness: 1646.71 spacedDyad: nCACsTGnyn motifConsensus: hCAmATTyyw 0.30 fitness: 1889.43 GADEM cycle[ 6] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: TbGAATGGAA 0.80 fitness: -1411.56 spacedDyad: nCACsTGnyn motifConsensus: TCAmAwrrAA 1.00 fitness: 706.62 spacedDyad: nCACsTGnyn motifConsensus: CCAAATrTCC 0.10 fitness: 1134.81 GADEM cycle[ 7] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: ACAGAArCwT 0.40 fitness: 958.14 spacedDyad: nCACsTGnyn motifConsensus: AmAGmwGTTT 0.50 fitness: 1449.59 spacedDyad: nCACsTGnyn motifConsensus: wAAAATGhmT 0.10 fitness: 1907.94 GADEM cycle[ 8] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: TCAwCTCTsw 0.70 fitness: 918.39 spacedDyad: nCACsTGnyn motifConsensus: hCAAAkrmwT 0.30 fitness: 1321.97 GADEM cycle[ 9] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: CCAGCTACTy 0.30 fitness: 952.20 spacedDyad: nCACsTGnyn motifConsensus: yywbTTTyCT 0.40 fitness: 1353.60 spacedDyad: nCACsTGnyn motifConsensus: nCAsmTGsCT 0.20 fitness: 2046.43 GADEM cycle[ 10] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: TCwCTksArm 0.40 fitness: 835.56 spacedDyad: nCACsTGnyn motifConsensus: TyrCTTGArs 0.20 fitness: 1457.83 spacedDyad: nCACsTGnyn motifConsensus: AswyTTGAAA 0.90 fitness: 1772.66 GADEM cycle[ 11] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: CyrTCTCTAC 0.10 fitness: 1039.03 spacedDyad: nCACsTGnyn motifConsensus: hCwTwTTTww 0.30 fitness: 1455.52 spacedDyad: nCACsTGnyn motifConsensus: TTwTATkwAw 0.60 fitness: 1457.29 GADEM cycle[ 12] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: TyTsyTTTrw 0.40 fitness: 1476.04 spacedDyad: nCACsTGnyn motifConsensus: yCTCTTyCyC 0.10 fitness: 2039.48 GADEM cycle[ 13] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: ryrCCTGTAA 0.10 fitness: 872.06 spacedDyad: nCACsTGnyn motifConsensus: AAAAywywsA 0.80 fitness: 1504.74 spacedDyad: nCACsTGnyn motifConsensus: AmAmCTswrA 0.30 fitness: 1558.83 GADEM cycle[ 14] generation[ 1] number of unique motif(s): 4 spacedDyad: nCACsTGnyn motifConsensus: CCAGCCTGGG 0.10 fitness: -1085.44 spacedDyad: nCACsTGnyn motifConsensus: wCTCyTTTkk 0.40 fitness: 1560.69 spacedDyad: nCACsTGnyn motifConsensus: TTTsyTswTk 1.00 fitness: 1745.99 spacedDyad: nCACsTGnyn motifConsensus: CCwCCyCwsC 0.20 fitness: 2095.19 GADEM cycle[ 15] generation[ 1] number of unique motif(s): 1 spacedDyad: nCACsTGnyn motifConsensus: yywGwwTTTA 0.60 fitness: 1315.49 GADEM cycle[ 16] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: wCArwATATT 0.70 fitness: 1265.71 spacedDyad: nCACsTGnyn motifConsensus: myAAAwkTAA 0.10 fitness: 1400.72 GADEM cycle[ 17] generation[ 1] number of unique motif(s): 4 spacedDyad: nCACsTGnyn motifConsensus: CCAGCACTTT 0.30 fitness: 869.63 spacedDyad: nCACsTGnyn motifConsensus: ymTGmwnTTT 0.20 fitness: 1340.46 spacedDyad: nCACsTGnyn motifConsensus: wwTsTkCAww 1.00 fitness: 1541.41 spacedDyad: nCACsTGnyn motifConsensus: wkTyTTGTTT 0.10 fitness: 1608.91 GADEM cycle[ 18] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: AmwrTTTTkr 0.50 fitness: 1171.61 spacedDyad: nCACsTGnyn motifConsensus: TCTyTTyATT 1.00 fitness: 1395.18 spacedDyad: nCACsTGnyn motifConsensus: mCAAATrTkw 0.10 fitness: 1499.42 GADEM cycle[ 19] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: wTTCmTTmww 0.30 fitness: 1372.05 spacedDyad: nCACsTGnyn motifConsensus: CywyTTksAr 0.60 fitness: 1446.63 spacedDyad: nCACsTGnyn motifConsensus: TCCCnTTTCC 0.10 fitness: 1502.19 GADEM cycle[ 20] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: CTTsCAGAwT 0.90 fitness: 1434.37 spacedDyad: nCACsTGnyn motifConsensus: nTTyCTGrrr 0.50 fitness: 1449.43 GADEM cycle[ 21] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: yCTbCTGrrd 0.40 fitness: 1199.75 spacedDyad: nCACsTGnyn motifConsensus: wmTGCTwAAT 1.00 fitness: 1340.88 GADEM cycle[ 22] generation[ 1] number of unique motif(s): 1 spacedDyad: nCACsTGnyn motifConsensus: wmwyATTrTk 0.50 fitness: 1364.34 GADEM cycle[ 23] generation[ 1] number of unique motif(s): 4 spacedDyad: nCACsTGnyn motifConsensus: CwwCwTwTAA 0.60 fitness: 1211.36 spacedDyad: nCACsTGnyn motifConsensus: CwCCATkTwr 0.30 fitness: 1279.72 spacedDyad: nCACsTGnyn motifConsensus: yAwTwTyTCw 0.70 fitness: 1475.39 spacedDyad: nCACsTGnyn motifConsensus: hmwTTTCCCw 0.90 fitness: 1655.63 GADEM cycle[ 24] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: wCwCATwmAy 0.30 fitness: 1301.14 spacedDyad: nCACsTGnyn motifConsensus: wCAswGwmAw 0.50 fitness: 1522.38 spacedDyad: nCACsTGnyn motifConsensus: wyTGTGrAAw 0.70 fitness: 1746.72 GADEM cycle[ 25] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: ymwTTTGkbw 0.40 fitness: 1407.38 spacedDyad: nCACsTGnyn motifConsensus: yCwCTGkGyy 0.20 fitness: 1451.87 spacedDyad: nCACsTGnyn motifConsensus: mCwCATGwkm 0.10 fitness: 1757.48 GADEM cycle[ 26] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: yhwyyTyCCA 0.30 fitness: 1226.53 spacedDyad: nCACsTGnyn motifConsensus: yyTkCTyymw 0.70 fitness: 1554.42 GADEM cycle[ 27] generation[ 1] number of unique motif(s): 4 spacedDyad: nCACsTGnyn motifConsensus: ACATCAsmAA 0.60 fitness: 1221.58 spacedDyad: nCACsTGnyn motifConsensus: wTwTTTrCAT 1.00 fitness: 1343.34 spacedDyad: nCACsTGnyn motifConsensus: mmAAAwsCmA 0.30 fitness: 1382.03 spacedDyad: nCACsTGnyn motifConsensus: sCTGCwGsCm 0.10 fitness: 2371.55 GADEM cycle[ 28] generation[ 1] number of unique motif(s): 1 spacedDyad: nCACsTGnyn motifConsensus: yCAkyTkhAw 0.30 fitness: 1200.53 GADEM cycle[ 29] generation[ 1] number of unique motif(s): 4 spacedDyad: nCACsTGnyn motifConsensus: mTwTTTryyA 0.20 fitness: 1162.56 spacedDyad: nCACsTGnyn motifConsensus: wmATywGCyA 0.10 fitness: 1448.43 spacedDyad: nCACsTGnyn motifConsensus: mAwsyTTTCw 0.80 fitness: 1498.43 spacedDyad: nCACsTGnyn motifConsensus: yyAsTTyCTm 0.90 fitness: 1751.05 GADEM cycle[ 30] generation[ 1] number of unique motif(s): 5 spacedDyad: nCACsTGnyn motifConsensus: yCwGCCTCCC 0.20 fitness: 361.24 spacedDyad: nCACsTGnyn motifConsensus: mywGCTyTGw 0.40 fitness: 1346.86 spacedDyad: nCACsTGnyn motifConsensus: CwTrTTCTCw 1.00 fitness: 1458.72 spacedDyad: nCACsTGnyn motifConsensus: CAAsAkrGCA 0.10 fitness: 1482.20 spacedDyad: nCACsTGnyn motifConsensus: yCwGyyTTyC 0.30 fitness: 1496.23 GADEM cycle[ 31] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: ywAsmTkTTT 0.60 fitness: 1207.89 spacedDyad: nCACsTGnyn motifConsensus: TTTmTTCCCT 1.00 fitness: 1283.89 spacedDyad: nCACsTGnyn motifConsensus: ymCyCTGyCm 0.10 fitness: 2109.44 GADEM cycle[ 32] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: TkAsmTnTTT 0.20 fitness: 1182.18 spacedDyad: nCACsTGnyn motifConsensus: TCAswwAyCm 0.10 fitness: 1507.59 spacedDyad: nCACsTGnyn motifConsensus: yywsTTCTTG 0.90 fitness: 1589.68 GADEM cycle[ 33] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: mhAvwTTTTG 0.20 fitness: 1176.32 spacedDyad: nCACsTGnyn motifConsensus: CCwnTTTTrr 0.40 fitness: 1373.77 GADEM cycle[ 34] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: wywTTTnCTk 0.70 fitness: 1093.47 spacedDyad: nCACsTGnyn motifConsensus: AmAkwTkCmw 0.10 fitness: 1245.63 spacedDyad: nCACsTGnyn motifConsensus: mCAGTkkATT 0.20 fitness: 1256.20 GADEM cycle[ 35] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: ywwryTGwrG 0.20 fitness: 1252.75 spacedDyad: nCACsTGnyn motifConsensus: yCwTTTACwG 0.80 fitness: 1276.80 spacedDyad: nCACsTGnyn motifConsensus: CCAsmTGsmm 0.10 fitness: 1595.93 GADEM cycle[ 36] generation[ 1] number of unique motif(s): 3 spacedDyad: nCACsTGnyn motifConsensus: yymTkTCTTw 0.90 fitness: 1418.28 spacedDyad: nCACsTGnyn motifConsensus: nvArCwCTGk 0.20 fitness: 1473.58 spacedDyad: nCACsTGnyn motifConsensus: CwCwyyCTkT 0.60 fitness: 1556.37 GADEM cycle[ 37] generation[ 1] number of unique motif(s): 1 spacedDyad: nCACsTGnyn motifConsensus: CywTTTswdG 0.30 fitness: 1072.47 GADEM cycle[ 38] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: myAksTTTkk 0.20 fitness: 1248.11 spacedDyad: nCACsTGnyn motifConsensus: CmAkGTyTkk 0.10 fitness: 1519.95 GADEM cycle[ 39] generation[ 1] number of unique motif(s): 1 spacedDyad: nCACsTGnyn motifConsensus: mCAsTwGAGk 0.20 fitness: 1442.21 GADEM cycle[ 40] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: ChmAsTGTGw 0.10 fitness: 1411.26 spacedDyad: nCACsTGnyn motifConsensus: mwwCyTGTGk 0.20 fitness: 1449.95 GADEM cycle[ 41] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: TCwGCThwTr 0.20 fitness: 1201.00 spacedDyad: nCACsTGnyn motifConsensus: yCAkywswGr 0.10 fitness: 1341.36 GADEM cycle[ 42] generation[ 1] number of unique motif(s): 1 spacedDyad: nCACsTGnyn motifConsensus: hyATTTyyTs 0.20 fitness: 1069.25 GADEM cycle[ 43] generation[ 1] number of unique motif(s): 1 spacedDyad: nCACsTGnyn motifConsensus: nTkGkksTTT 0.10 fitness: 1268.41 GADEM cycle[ 44] generation[ 1] number of unique motif(s): 2 spacedDyad: nCACsTGnyn motifConsensus: mwwwATCCmT 0.80 fitness: 1187.15 spacedDyad: nCACsTGnyn motifConsensus: GCTkyTsTkn 0.10 fitness: 1627.13 GADEM cycle[ 45] generation[ 1] number of unique motif(s): 1 spacedDyad: nCACsTGnyn motifConsensus: mwwwATCCmT 0.90 fitness: 1266.17 finished: Sun Jul 18 23:10:42 2010 approximated processor time in seconds: 62220.000000