processor ID: 16649 ========================================================================== |------------------------------------------------------------------| | | | *** 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_NFkB_M00280/a/HS1235-p1em6_3642-selfUnion-pm400bp.hg18.20100718.fa.3stage_dm_w4.fa.pwmNFkB_M00208.mx.weight0.de_novo -minN 500 -ev 5000 -pv 0.0002 -fpwm0 /home/grobertson/Fi/PWMs/NFkB_M00208.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/NFkB_M00208.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/NFkB_M00208.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 05:59:36 2010 ========================================================================= GADEM cycle[ 1] generation[ 1] number of unique motif(s): 1 spacedDyad: rGGGAyTTTCCm motifConsensus: TTTnywTTTTyw 1.00 fitness: 49.34 GADEM cycle[ 2] generation[ 1] number of unique motif(s): 1 spacedDyad: rGGGAyTTTCCm motifConsensus: wwwwwTTTwwAw 0.40 fitness: 1499.63 GADEM cycle[ 3] generation[ 1] number of unique motif(s): 2 spacedDyad: rGGGAyTTTCCm motifConsensus: AAGAGwGTTTCA 0.10 fitness: 608.96 spacedDyad: rGGGAyTTTCCm motifConsensus: AwdwywTTTyCT 0.70 fitness: 1681.35 GADEM cycle[ 4] generation[ 1] number of unique motif(s): 2 spacedDyad: rGGGAyTTTCCm motifConsensus: TyTnnTTTTywT 0.80 fitness: 1207.25 spacedDyad: rGGGAyTTTCCm motifConsensus: AGrAAkGTTmAA 0.10 fitness: 1683.52 GADEM cycle[ 5] generation[ 1] number of unique motif(s): 1 spacedDyad: rGGGAyTTTCCm motifConsensus: TswkwwTTTwmw 0.40 fitness: 1531.45 GADEM cycle[ 6] generation[ 1] number of unique motif(s): 2 spacedDyad: rGGGAyTTTCCm motifConsensus: ATTCCATTCsAT 1.00 fitness: -2605.72 spacedDyad: rGGGAyTTTCCm motifConsensus: wwwyATTThwsw 0.40 fitness: 1483.50 GADEM cycle[ 7] generation[ 1] number of unique motif(s): 3 spacedDyad: rGGGAyTTTCCm motifConsensus: wkynwTyCTyyT 0.40 fitness: 912.83 spacedDyad: rGGGAyTTTCCm motifConsensus: TAGAATCTGCAA 0.20 fitness: 917.21 spacedDyad: rGGGAyTTTCCm motifConsensus: yTkyTTTCyyyw 1.00 fitness: 1629.31 GADEM cycle[ 8] generation[ 1] number of unique motif(s): 2 spacedDyad: rGGGAyTTTCCm motifConsensus: wkGnwTTTTrww 0.30 fitness: 1580.49 spacedDyad: rGGGAyTTTCCm motifConsensus: AAAsAsAwwwww 0.80 fitness: 1746.65 GADEM cycle[ 9] generation[ 1] number of unique motif(s): 2 spacedDyad: rGGGAyTTTCCm motifConsensus: GAAGCATTCTCA 0.20 fitness: 76.48 spacedDyad: rGGGAyTTTCCm motifConsensus: AGAAACTTCTTT 0.40 fitness: 856.23 GADEM cycle[ 10] generation[ 1] number of unique motif(s): 2 spacedDyad: rGGGAyTTTCCm motifConsensus: wrwkAAAwTmww 0.10 fitness: 1397.25 spacedDyad: rGGGAyTTTCCm motifConsensus: AmAnAwwTymmA 0.20 fitness: 1629.15 GADEM cycle[ 11] generation[ 1] number of unique motif(s): 3 spacedDyad: rGGGAyTTTCCm motifConsensus: wyCCynTyTCym 0.40 fitness: 326.04 spacedDyad: rGGGAyTTTCCm motifConsensus: wwwkyyTnmAAA 0.80 fitness: 1518.21 spacedDyad: rGGGAyTTTCCm motifConsensus: wwkAAAwCTnyw 0.10 fitness: 1890.69 GADEM cycle[ 12] generation[ 1] number of unique motif(s): 4 spacedDyad: rGGGAyTTTCCm motifConsensus: TGGCwCAyrCCT 0.10 fitness: 122.16 spacedDyad: rGGGAyTTTCCm motifConsensus: TGTGwGTTGArT 0.90 fitness: 1014.56 spacedDyad: rGGGAyTTTCCm motifConsensus: wksywCATTTyw 0.50 fitness: 1752.47 spacedDyad: rGGGAyTTTCCm motifConsensus: wkTyTCwkyyyT 0.60 fitness: 2186.95 GADEM cycle[ 13] generation[ 1] number of unique motif(s): 2 spacedDyad: rGGGAyTTTCCm motifConsensus: rrGAAyATTywn 0.10 fitness: 1700.92 spacedDyad: rGGGAyTTTCCm motifConsensus: wkkymyTTyyCw 0.30 fitness: 1761.30 GADEM cycle[ 14] generation[ 1] number of unique motif(s): 1 spacedDyad: rGGGAyTTTCCm motifConsensus: wyTknyTTyywG 0.30 fitness: 1244.42 GADEM cycle[ 15] generation[ 1] number of unique motif(s): 3 spacedDyad: rGGGAyTTTCCm motifConsensus: TCnGCCTCCyrr 0.50 fitness: -2608.62 spacedDyad: rGGGAyTTTCCm motifConsensus: wwTkTTTsTwww 0.70 fitness: 1344.65 spacedDyad: rGGGAyTTTCCm motifConsensus: wrwGswTTTmww 0.30 fitness: 1459.42 GADEM cycle[ 16] generation[ 1] number of unique motif(s): 3 spacedDyad: rGGGAyTTTCCm motifConsensus: wnwkTyTyymmA 0.30 fitness: 1414.22 spacedDyad: rGGGAyTTTCCm motifConsensus: AwkCwywsmAAA 1.00 fitness: 1615.82 spacedDyad: rGGGAyTTTCCm motifConsensus: mAGGArTTymAG 0.10 fitness: 1987.52 GADEM cycle[ 17] generation[ 1] number of unique motif(s): 3 spacedDyad: rGGGAyTTTCCm motifConsensus: wTTTmywmATTT 0.70 fitness: 1545.26 spacedDyad: rGGGAyTTTCCm motifConsensus: wsTGAyTymhmw 0.10 fitness: 1658.24 spacedDyad: rGGGAyTTTCCm motifConsensus: TsTGbyTyyTsy 0.30 fitness: 1680.90 GADEM cycle[ 18] generation[ 1] number of unique motif(s): 2 spacedDyad: rGGGAyTTTCCm motifConsensus: TkTnywTrTkww 0.40 fitness: 1349.85 spacedDyad: rGGGAyTTTCCm motifConsensus: wkkbyyTsyyyy 0.30 fitness: 1630.78 GADEM cycle[ 19] generation[ 1] number of unique motif(s): 4 spacedDyad: rGGGAyTTTCCm motifConsensus: TGGAyATTTGGA 0.30 fitness: 675.46 spacedDyad: rGGGAyTTTCCm motifConsensus: wrrCwmTTTkhw 0.10 fitness: 1410.83 spacedDyad: rGGGAyTTTCCm motifConsensus: wTwkTywCwGAA 0.50 fitness: 1421.85 spacedDyad: rGGGAyTTTCCm motifConsensus: wTTCAsmAwrwT 0.80 fitness: 1467.90 GADEM cycle[ 20] generation[ 1] number of unique motif(s): 4 spacedDyad: rGGGAyTTTCCm motifConsensus: wGwrvyTyTbmw 0.20 fitness: 1257.44 spacedDyad: rGGGAyTTTCCm motifConsensus: wrTGmywTTkww 0.40 fitness: 1399.31 spacedDyad: rGGGAyTTTCCm motifConsensus: TGTdywCwTTww 0.50 fitness: 1404.06 spacedDyad: rGGGAyTTTCCm motifConsensus: wGrywwCATwwT 1.00 fitness: 1562.62 GADEM cycle[ 21] generation[ 1] number of unique motif(s): 3 spacedDyad: rGGGAyTTTCCm motifConsensus: wkGsAkwATwww 0.90 fitness: 1338.63 spacedDyad: rGGGAyTTTCCm motifConsensus: ywrmwGTTTmmw 0.20 fitness: 1470.31 spacedDyad: rGGGAyTTTCCm motifConsensus: wGrrArwkkmwG 0.10 fitness: 1666.81 GADEM cycle[ 22] generation[ 1] number of unique motif(s): 3 spacedDyad: rGGGAyTTTCCm motifConsensus: AkGywTTATTww 0.60 fitness: 1255.05 spacedDyad: rGGGAyTTTCCm motifConsensus: ATGsAmwCATCA 0.30 fitness: 1437.95 spacedDyad: rGGGAyTTTCCm motifConsensus: rrkGArryymCA 0.10 fitness: 2163.19 GADEM cycle[ 23] generation[ 1] number of unique motif(s): 4 spacedDyad: rGGGAyTTTCCm motifConsensus: AATCCCAGCwmy 0.30 fitness: -973.12 spacedDyad: rGGGAyTTTCCm motifConsensus: wkGywTTATThw 0.60 fitness: 1268.42 spacedDyad: rGGGAyTTTCCm motifConsensus: mArnTyTTCyyw 0.20 fitness: 1571.51 spacedDyad: rGGGAyTTTCCm motifConsensus: ArrCmyTTyCTn 0.10 fitness: 1822.03 GADEM cycle[ 24] generation[ 1] number of unique motif(s): 3 spacedDyad: rGGGAyTTTCCm motifConsensus: yrGCTCACTGCA 0.10 fitness: 346.59 spacedDyad: rGGGAyTTTCCm motifConsensus: TkknTTTATmyw 0.20 fitness: 1187.08 spacedDyad: rGGGAyTTTCCm motifConsensus: wdGnCAAATAww 0.50 fitness: 1362.57 GADEM cycle[ 25] generation[ 1] number of unique motif(s): 2 spacedDyad: rGGGAyTTTCCm motifConsensus: wAGGCCwCAAAG 0.90 fitness: 1273.20 spacedDyad: rGGGAyTTTCCm motifConsensus: wGGnTkyChmmA 0.10 fitness: 1784.50 GADEM cycle[ 26] generation[ 1] number of unique motif(s): 2 spacedDyad: rGGGAyTTTCCm motifConsensus: wkrCmAAAwwwT 0.20 fitness: 1276.35 spacedDyad: rGGGAyTTTCCm motifConsensus: TkknACArAwrw 0.70 fitness: 1610.72 GADEM cycle[ 27] generation[ 1] number of unique motif(s): 1 spacedDyad: rGGGAyTTTCCm motifConsensus: TTTsAyAGAGCA 0.40 fitness: 782.05 GADEM cycle[ 28] generation[ 1] number of unique motif(s): 1 spacedDyad: rGGGAyTTTCCm motifConsensus: TkwmmCwnAAAA 0.50 fitness: 1288.95 finished: Sun Jul 18 18:38:03 2010 approximated processor time in seconds: 45507.000000