processor ID: 15427 ========================================================================== |------------------------------------------------------------------| | | | *** Running a seeded analysis *** | | | |------------------------------------------------------------------| command line: /home/grobertson/Fi/Code/20090926_v1.3/Fi_v1.3/bin/fi -fseq /projects/remc_bigdata/Karsan/HS1238_kd/compare/FA/HS1238-cmp-lowP_17000-sU.hg18.fa.3stage_dm_w4.fa -fout /projects/remc_bigdata/Karsan/HS1238_kd/compare/seed_CSL_TGTGGGAA/b/HS1238-cmp-lowP_17000-sU.hg18.fa.3stage_dm_w4.fa.pwmCSL_TGTGGGAA.mx.weight0.de_novo -minN 2000 -ev 5000 -pv 0.0002 -fpwm0 /home/grobertson/Fi/PWMs/CSL_TGTGGGAA.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/HS1238_kd/compare/FA/HS1238-cmp-lowP_17000-sU.hg18.fa.3stage_dm_w4.fa number of sequences in input file: 17000 average sequence length: 1085 total number of nucleotides: 18455169 max number of generations: 1 population size: 10 use a user-specified pwm as the seed /home/grobertson/Fi/PWMs/CSL_TGTGGGAA.mx fraction (number) input sequences subject to EM 1.00 (17000) 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_TGTGGGAA.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: 2000 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 11 12:45:57 2010 ========================================================================= GADEM cycle[ 1] generation[ 1] number of unique motif(s): 1 spacedDyad: nnTGTGGGAAnn motifConsensus: rnkGwGGsAGGr 1.00 fitness: -16596.09 GADEM cycle[ 2] generation[ 1] number of unique motif(s): 1 spacedDyad: nnTGTGGGAAnn motifConsensus: ArrrrArrrAAr 1.00 fitness: -4739.92