---
Config:
  version:  4.15
  heu_dir:  heu_dir
  def_cfg:  gmes.cfg
  gm_hmm:   gmhmme3
  log_file: gmes.log
  run_cfg:  run.cfg
  bin:      ''
  work_dir: ''

Parameters:
  max_contig: 5000000
  min_contig:   50000
  max_gap:       5000
  max_mask:      5000
  soft_mask: 0
  min_contig_prediction: 500
  min_gene_prediction:   300
  ES:        0
  fungus:    0
  ET:       ''
  et_score:  4
  sequence: ''
  evidence: ''
  ini_mod:  ''
  usr_cfg:  ''
  out: ''
  test_set: ''
  pbs:       0
  cores:     1
  max_intergenic: 0
  v:        ''
  debug:    ''

Run:
  set_dirs:             1
  commit_input_data:    1
  input_data_report:    1
  commit_training_data: 1
  training_data_report: 1
  prepare_ini_mod:      1
  run_training:         1
  training_report:      0
  run_prediction:       1
  prediction_report:    0

ES_ini:
  mod: es_ini.mod
  parse_dir: ''

ES_A:
  iterations: 2
  in_mod:  ini.mod
  out_mod: ES_A.mod
  run_prediction: 1
  run_training:   1
  set_in: set.out
  min_cds: 800
  parse_dir: .
  parse_out: parse.es_a
  cod:           cod.seq
  non:           non.seq
  start:       start.seq
  stop_taa: stop_taa.seq
  stop_tag: stop_tag.seq
  stop_tga: stop_tga.seq
  don:           don.seq
  acc:           acc.seq

ES_B:
  iterations: 1
  in_mod:  ES_A.mod
  out_mod: ES_B.mod
  run_prediction: 1
  run_training:   1
  set_in: set.out
  min_cds: 800
  parse_dir: .
  parse_out: parse.es_b
  cod:           cod.seq
  non:           non.seq
  start:       start.seq
  stop_taa: stop_taa.seq
  stop_tag: stop_tag.seq
  stop_tga: stop_tga.seq
  don:           don.seq
  acc:           acc.seq
  intron_len:     intron.len
  initial_len:   initial.len
  internal_len: internal.len
  terminal_len: terminal.len
  single_len:     single.len

ES_C:
  iterations: 4
  in_mod:  ES_B.mod
  out_mod: ES_C.mod
  run_prediction: 1
  run_training:   1
  set_in: set.out
  min_cds: 800
  parse_dir: .
  parse_out: parse.es_c
  cod:           cod.seq
  non:           non.seq
  start:       start.seq
  stop_taa: stop_taa.seq
  stop_tag: stop_tag.seq
  stop_tga: stop_tga.seq
  don:           don.seq
  acc:           acc.seq
  intron_len:     intron.len
  initial_len:   initial.len
  internal_len: internal.len
  terminal_len: terminal.len
  single_len:     single.len
  phase:         exon_phase.mod
  tr_s_vs_m: transition_s_m.mod
  tr_i_vs_t: transition_i_t.mod
  bp_region: bp_region.seq
  bp_region_length: 50
  acc_short: acc_short.seq
  gibbs_seq: gibbs.seq
  gibbs_seq_max: 4000
  tr_bp: transition_bp.mod

ET_ini:
  mod: et_ini.mod
  parse_dir: ''
  seq_in:     training.fna
  introns_in: et_training.gff
  parse_out:  parse.et_ini
  et_score:   4
  don: don.seq
  acc: acc.seq
  intron_len: intron.len
  acc_short: acc_short.seq
  bp_region: bp_region.seq
  gibbs_seq: gibbs.seq
  bp_region_length: 50
  gibbs_seq_max:  4000
  tr_bp: transition_bp.mod

ET_A:
  iterations: 1
  in_mod:  ini.mod
  out_mod: ET_A.mod
  run_prediction: 1
  run_training: 1
  set_in: set.out
  introns_in: ../../data/et_training.gff
  parse_dir: .
  parse_out: parse.et_a
  cod:           cod.seq
  non:           non.seq
  start:       start.seq
  stop_taa: stop_taa.seq
  stop_tag: stop_tag.seq
  stop_tga: stop_tga.seq

ET_B:
  iterations: 1
  in_mod:  ET_A.mod
  out_mod: ET_B.mod
  run_prediction: 1
  run_training: 1
  set_in: set.out
  introns_in: ../../data/et_training.gff
  parse_dir: .
  parse_out: parse.et_b
  cod:           cod.seq
  non:           non.seq
  start:       start.seq
  stop_taa: stop_taa.seq
  stop_tag: stop_tag.seq
  stop_tga: stop_tga.seq
  initial_len:  initial.len
  internal_len: internal.len
  terminal_len: terminal.len
  single_len:     single.len

ET_C:
  iterations: 2
  in_mod:  ET_B.mod
  out_mod: ET_C.mod
  run_prediction: 1
  run_training: 1
  set_in: set.out
  introns_in: ../../data/et_training.gff
  parse_dir: .
  parse_out: parse.et_c
  cod:           cod.seq
  non:           non.seq
  start:       start.seq
  stop_taa: stop_taa.seq
  stop_tag: stop_tag.seq
  stop_tga: stop_tga.seq
  initial_len:   initial.len
  internal_len: internal.len
  terminal_len: terminal.len
  single_len:     single.len
  don:           don.seq
  acc:           acc.seq
  phase:         exon_phase.mod
  tr_s_vs_m: transition_s_m.mod
  tr_i_vs_t: transition_i_t.mod
  acc_short: acc_short.seq

single_DUR:
  min: 300
  max: 10000
  in: ''
  out: single.dur
  com: k
  scale3: 1
  gamma: '2,350'

intron_DUR:
  min: 20
  max: 10000
  in: intron.len
  out: intron.dur
  com: kw
  W: 3

initial_DUR:
  min: 3
  max: 10000
  in: initial.len
  out: initial.dur
  com: kw
  smooth3: 1

internal_DUR:
  min: 3
  max: 10000
  in: internal.len
  out: internal.dur
  com: kw
  smooth3: 1 

terminal_DUR:
  min: 3
  max: 10000
  in: terminal.len
  out: terminal.dur
  com: kw
  smooth3: 1

spacer_DUR:
  min: 2
  max: 40
  in: spacer.len
  out: spacer.dur
  com: kw
  W: 3

prespacer_DUR:
  min: 5
  max: 3000
  in: prespacer.len
  out: prespacer.dur
  com: kw
  W: 3

branch_point:
  infile: bp.seq
  outfile: BP.mat
  format_out: ''
  order: 0
  auto_order: 1
  threshold_zero: 2000
  pseudocounts: 10
  type: ''
  width: 9
  margin: 9
  site_size: 0
  phase: ''
  gc_low: -1
  gc_high: -1
  quite: 0

acceptor_short_AG:
  infile: acc_short.seq
  outfile: AG_SHORT.mat
  format_out: ''
  order: 0
  auto_order: 1
  threshold_zero: 2000
  pseudocounts: 10
  type: AG
  width: 5
  margin: 2
  site_size: 2
  phase: ''
  gc_low: -1
  gc_high: -1
  quite: 0

acceptor_AG:
  infile: acc.seq
  outfile: AG.mat
  format_out: ''
  order: 0
  auto_order: 1
  threshold_zero: 2000
  pseudocounts: 10
  type: AG
  width: 21
  margin: 18
  site_size: 2
  phase: ''
  gc_low: -1
  gc_high: -1
  quite: 0

donor_GT:
  infile: don.seq
  outfile: GT.mat
  format_out: ''
  order: 0
  auto_order: 1
  threshold_zero: 2000
  pseudocounts: 10
  type: GT
  width: 9
  margin: 3
  site_size: 2
  phase: ''
  gc_low: -1
  gc_high: -1
  quite: 0

start_ATG:
  infile: start.seq
  outfile: ATG.mat
  format_out: ''
  order: 0
  auto_order: 1
  threshold_zero: 2000
  pseudocounts: 10
  type: ATG
  width: 12
  margin: 6
  site_size: 3
  phase: ''
  gc_low: -1
  gc_high: -1
  quite: 0

stop_TAA:
  infile: stop_taa.seq
  outfile: TAA.mat
  format_out: ''
  order: 0
  auto_order: 1
  threshold_zero: 2000
  pseudocounts: 10
  type: TAA
  width: 12
  margin: 3
  site_size: 3
  phase: ''
  gc_low: -1
  gc_high: -1
  quite: 1

stop_TAG:
  infile: stop_tag.seq
  outfile: TAG.mat
  format_out: ''
  order: 0
  auto_order: 1
  threshold_zero: 2000
  pseudocounts: 10
  type: TAG
  width: 12
  margin: 3
  site_size: 3
  phase: ''
  gc_low: -1
  gc_high: -1
  quite: 1

stop_TGA:
  infile: stop_tga.seq
  outfile: TGA.mat
  format_out: ''
  order: 0
  auto_order: 1
  threshold_zero: 2000
  pseudocounts: 10
  type: TGA
  width: 12
  margin: 3
  site_size: 3
  phase: ''
  gc_low: -1
  gc_high: -1
  quite: 1

user_GMHMM3_parameters:
  ORGANISM: -1
  ORDER: -1
  N_PROB_NON: -1
  N_PROB_COD: -1
  SINGLE_MAX:  -1
  SINGLE_MIN:  -1
  SINGLE_TAG:  -1
  SINGLE_TYPE: -1
  INITIAL_MAX:  -1
  INITIAL_MIN:  -1
  INITIAL_TAG:  -1
  INITIAL_TYPE: -1
  EXON_MAX:  -1
  EXON_MIN:  -1
  EXON_TAG:  -1
  EXON_TYPE: -1
  TERMINAL_MAX:  -1
  TERMINAL_MIN:  -1
  TERMINAL_TAG:  -1
  TERMINAL_TYPE: -1
  INTRON_MAX:  -1
  INTRON_MIN:  -1
  INTRON_TAG:  -1
  INTRON_TYPE: -1
  INTERGENIC_MAX:  -1
  INTERGENIC_MIN:  -1
  INTERGENIC_TAG:  -1
  INTERGENIC_TYPE: -1
  INITIAL_EXON_PHASE:  -1
  TERMINAL_EXON_PHASE: -1
  INTERNAL_EXON_PHASE: -1
  ToSingleGene: -1
  ToMultiGene:  -1
  ToInternalExon: -1
  ToTerminalExon: -1
  NORM_SITES: -1
  INI_WIDTH:    -1
  INI_MARGIN:   -1
  INI_ORDER:    -1
  INI_WIDTH_P:  -1
  INI_MARGIN_P: -1
  TERM_TAA_WIDTH:    -1
  TERM_TAA_MARGIN:   -1
  TERM_TAA_ORDER:    -1
  TERM_TAA_WIDTH_P:  -1
  TERM_TAA_MARGIN_P: -1
  TERM_TAG_WIDTH:    -1
  TERM_TAG_MARGIN:   -1
  TERM_TAG_ORDER:    -1
  TERM_TAG_WIDTH_P:  -1
  TERM_TAG_MARGIN_P: -1
  TERM_TGA_WIDTH:    -1
  TERM_TGA_MARGIN:   -1
  TERM_TGA_ORDER:    -1
  TERM_TGA_WIDTH_P:  -1
  TERM_TGA_MARGIN_P: -1
  DONOR_0_WIDTH:    -1
  DONOR_0_MARGIN:   -1
  DONOR_0_ORDER:    -1
  DONOR_0_WIDTH_P:  -1
  DONOR_0_MARGIN_P: -1
  DONOR_1_WIDTH:    -1
  DONOR_1_MARGIN:   -1
  DONOR_1_ORDER:    -1
  DONOR_1_WIDTH_P:  -1
  DONOR_1_MARGIN_P: -1
  DONOR_2_WIDTH:    -1
  DONOR_2_MARGIN:   -1
  DONOR_2_ORDER:    -1
  DONOR_2_WIDTH_P:  -1
  DONOR_2_MARGIN_P: -1
  ACCEPTOR_0_WIDTH:    -1
  ACCEPTOR_0_MARGIN:   -1
  ACCEPTOR_0_ORDER:    -1
  ACCEPTOR_0_WIDTH_P:  -1
  ACCEPTOR_0_MARGIN_P: -1
  ACCEPTOR_1_WIDTH:    -1
  ACCEPTOR_1_MARGIN:   -1
  ACCEPTOR_1_ORDER:    -1
  ACCEPTOR_1_WIDTH_P:  -1
  ACCEPTOR_1_MARGIN_P: -1
  ACCEPTOR_2_WIDTH:    -1
  ACCEPTOR_2_MARGIN:   -1
  ACCEPTOR_2_ORDER:    -1
  ACCEPTOR_2_WIDTH_P:  -1
  ACCEPTOR_2_MARGIN_P: -1
  INI_MAT:        -1
  TERM_TAA_MAT:   -1
  TERM_TAG_MAT:   -1
  TERM_TGA_MAT:   -1
  DONOR_0_MAT:    -1
  DONOR_1_MAT:    -1
  DONOR_2_MAT:    -1
  ACCEPTOR_0_MAT: -1
  ACCEPTOR_1_MAT: -1
  ACCEPTOR_2_MAT: -1
  BP: -1
  LIMIT_BP_DURATION: -1
  TO_BP:     -1
  AROUND_BP: -1
  BP_SPACER_ORDER:  -1
  MARKOV_BP_SPACER: -1
  BRANCH_WIDTH:    -1
  BRANCH_MARGIN:   -1
  BRANCH_ORDER:    -1
  BRANCH_WIDTH_P:  -1
  BRANCH_MARGIN_P: -1
  BRANCH_MAT:      -1
  BP_ACC_MIN:   -1
  BP_ACC_MAX:   -1
  BP_ACC_TAG:   -1
  BP_ACC_TYPE:  -1
  BP_ACC_DISTR: -1
  DON_BP_MAX:  -1
  DON_BP_MIN:  -1
  DON_BP_TAG:  -1
  DON_BP_TYPE: -1
  ACC_BP_0_WIDTH:  -1
  ACC_BP_0_MARGIN: -1
  ACC_BP_0_ORDER:  -1
  ACC_BP_1_WIDTH:  -1
  ACC_BP_1_MARGIN: -1
  ACC_BP_1_ORDER:  -1
  ACC_BP_2_WIDTH:  -1
  ACC_BP_2_MARGIN: -1
  ACC_BP_2_ORDER:  -1
  ACC_BP_0_MAT: -1
  ACC_BP_1_MAT: -1
  ACC_BP_2_MAT: -1
  DON_BP_DISTR: -1
  MARKOV: -1
  SINGLE_DISTR:     -1
  INITIAL_DISTR:    -1
  EXON_DISTR:       -1
  TERMINAL_DISTR:   -1
  INTRON_DISTR:     -1
  INTERGENIC_DISTR: -1

GMHMM3_order_basic:
  1:   ORGANISM
  2:   ORDER
  3:   N_PROB_NON
  4:   N_PROB_COD
  5:   SINGLE_MAX
  6:   SINGLE_MIN
  7:   SINGLE_TAG
  8:   SINGLE_TYPE
  9:   INITIAL_MAX
  10:  INITIAL_MIN
  11:  INITIAL_TAG
  12:  INITIAL_TYPE
  13:  EXON_MAX
  14:  EXON_MIN
  15:  EXON_TAG
  16:  EXON_TYPE
  17:  TERMINAL_MAX
  18:  TERMINAL_MIN
  19:  TERMINAL_TAG
  20:  TERMINAL_TYPE
  21:  INTRON_MAX
  22:  INTRON_MIN
  23:  INTRON_TAG
  24:  INTRON_TYPE
  25:  INTERGENIC_MAX
  26:  INTERGENIC_MIN
  27:  INTERGENIC_TAG
  28:  INTERGENIC_TYPE
  29:  INITIAL_EXON_PHASE
  30:  TERMINAL_EXON_PHASE
  31:  INTERNAL_EXON_PHASE
  32:  ToSingleGene
  33:  ToMultiGene
  34:  ToInternalExon
  35:  ToTerminalExon
  36:  NORM_SITES
  37:  INI_WIDTH
  38:  INI_MARGIN
  39:  INI_ORDER
  40:  INI_WIDTH_P
  41:  INI_MARGIN_P
  42:  TERM_TAA_WIDTH
  43:  TERM_TAA_MARGIN
  44:  TERM_TAA_ORDER
  45:  TERM_TAA_WIDTH_P
  46:  TERM_TAA_MARGIN_P
  47:  TERM_TAG_WIDTH
  48:  TERM_TAG_MARGIN
  49:  TERM_TAG_ORDER
  50:  TERM_TAG_WIDTH_P
  51:  TERM_TAG_MARGIN_P
  52:  TERM_TGA_WIDTH
  53:  TERM_TGA_MARGIN
  54:  TERM_TGA_ORDER
  56:  TERM_TGA_WIDTH_P
  57:  TERM_TGA_MARGIN_P
  58:  DONOR_0_WIDTH
  59:  DONOR_0_MARGIN
  60:  DONOR_0_ORDER
  61:  DONOR_0_WIDTH_P
  62:  DONOR_0_MARGIN_P
  63:  DONOR_1_WIDTH
  64:  DONOR_1_MARGIN
  65:  DONOR_1_ORDER
  66:  DONOR_1_WIDTH_P
  67:  DONOR_1_MARGIN_P
  68:  DONOR_2_WIDTH
  69:  DONOR_2_MARGIN
  70:  DONOR_2_ORDER
  71:  DONOR_2_WIDTH_P
  72:  DONOR_2_MARGIN_P
  73:  ACCEPTOR_0_WIDTH
  74:  ACCEPTOR_0_MARGIN
  75:  ACCEPTOR_0_ORDER
  76:  ACCEPTOR_0_WIDTH_P
  77:  ACCEPTOR_0_MARGIN_P
  78:  ACCEPTOR_1_WIDTH
  79:  ACCEPTOR_1_MARGIN
  80:  ACCEPTOR_1_ORDER
  81:  ACCEPTOR_1_WIDTH_P
  82:  ACCEPTOR_1_MARGIN_P
  83:  ACCEPTOR_2_WIDTH
  84:  ACCEPTOR_2_MARGIN
  85:  ACCEPTOR_2_ORDER
  86:  ACCEPTOR_2_WIDTH_P
  87:  ACCEPTOR_2_MARGIN_P
  88:  INI_MAT
  89:  TERM_TAA_MAT
  90:  TERM_TAG_MAT
  91:  TERM_TGA_MAT
  92:  DONOR_0_MAT
  93:  DONOR_1_MAT
  94:  DONOR_2_MAT
  95:  ACCEPTOR_0_MAT
  96:  ACCEPTOR_1_MAT
  97:  ACCEPTOR_2_MAT
  298: MARKOV
  299: SINGLE_DISTR
  300: INITIAL_DISTR
  301: EXON_DISTR
  302: TERMINAL_DISTR
  303: INTRON_DISTR
  304: INTERGENIC_DISTR

GMHMM3_order_BP:
  201:  BP
  202:  LIMIT_BP_DURATION
  203:  TO_BP
  204:  AROUND_BP
  205:  BRANCH_WIDTH
  206:  BRANCH_MARGIN
  207:  BRANCH_ORDER
  208:  BRANCH_WIDTH_P
  209:  BRANCH_MARGIN_P
  210:  BRANCH_MAT
  211:  BP_SPACER_ORDER
  212:  MARKOV_BP_SPACER
  213:  BP_ACC_MIN
  214:  BP_ACC_MAX
  215:  BP_ACC_TAG
  216:  BP_ACC_TYPE
  217:  BP_ACC_DISTR
  218:  DON_BP_MAX
  219:  DON_BP_MIN
  220:  DON_BP_TAG
  221:  DON_BP_TYPE
  222:  ACC_BP_0_WIDTH
  223:  ACC_BP_0_MARGIN
  224:  ACC_BP_0_ORDER
  225:  ACC_BP_1_WIDTH
  226:  ACC_BP_1_MARGIN
  227:  ACC_BP_1_ORDER
  228:  ACC_BP_2_WIDTH
  229:  ACC_BP_2_MARGIN
  230:  ACC_BP_2_ORDER
  231:  ACC_BP_0_MAT
  232:  ACC_BP_1_MAT
  233:  ACC_BP_2_MAT
  400: DON_BP_DISTR

