processor ID: 17939
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|              *** Running a seeded analysis ***                   |
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command line: /home/grobertson/Fi/Code/20110605/GADEM_v1.3.1/bin/gadem -fseq /projects/remc_bigdata/Karsan/motifs/20110604/NFKB-ChIP-seq.score-300.L-100.12381-seqs.hg18.fa -fpwm0 /home/grobertson/Fi/PWMs/NFKB1_JASPAR_MA0105.mx -minN 6000 -maskR 1 -fout /projects/remc_bigdata/Karsan/motifs/20110604/report.txt -verbose 1 -nbs 20 

Data:
  input (ChIP) sequence file:				/projects/remc_bigdata/Karsan/motifs/20110604/NFKB-ChIP-seq.score-300.L-100.12381-seqs.hg18.fa
  number of sequences in input file:			12381
  average sequence length:				737
  total number of nucleotides:				9133212
  [a,c,g,t] frequencies:				0.2280 0.2720 0.2720 0.2280

Motif model:
  use the user-specified pwm as the starting PWM	/home/grobertson/Fi/PWMs/NFKB1_JASPAR_MA0105.mx

  This pwm is repeatedly used as the starting PWMf for the EM algorithm. Similar
  (motif variants) or different motifs may be identified. To identify motif vaiants
  set -ev large, e.g., 10000 and -minN small, e.g., numSeq/10. This allows gadem
  to identify motif variants that are present in at least 10 percent of the
  sequences. A large log(E-value) cutoff enures such motifs are found.

Background model:
  background model estimated from the input data:	/projects/remc_bigdata/Karsan/motifs/20110604/NFKB-ChIP-seq.score-300.L-100.12381-seqs.hg18.fa
  							0.228050 0.271950 0.271950 0.228050
  background Markov order:				0th

Declaring BINDING SITES:
  pwm score p-value cutoff for declaring binding site:	2.500000e-04
  null pwm log-likelihood ratio score distribution deterimined using:
    Staden probability generating function method (Comput. Appl. Biosci., 5,89,1989).

Declaring MOTIFS:
  motif p-value (significance of alignment) is computed using the subroutine from MEME
  log(E-value) cutoff:					 0.00

Motif prior probability type:
  motif prior probability type (see documentation):	1 (gaussian motif location prior)

Genetic Algorithm (GA):
  running a seeded analysis - GA not needed.

EM:
  maximal number of EM steps:				40
  EM convergence criterion:				1.000000e-04
  fraction (number) input sequences subject to EM	1.00 (12381)

MAXP value:
  run EM on the starting pwm /home/grobertson/Fi/PWMs/NFKB1_JASPAR_MA0105.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).

Other parameters:
  simple repeats such as 'aaaaaaaa' (see usage) are masked before running GADEM
  minimal no. sites for each motif:			6000
  base extension and trimming?				yes

job started: Sun Jun  5 07:15:53 2011

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