Will create parameters for a EUKARYOTIC species!
creating directory /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/ab_initio_parameters/augustus/species/plecoglossus_altivelis/ ...
creating /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/ab_initio_parameters/augustus/species/plecoglossus_altivelis/plecoglossus_altivelis_parameters.cfg ...
creating /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/ab_initio_parameters/augustus/species/plecoglossus_altivelis/plecoglossus_altivelis_weightmatrix.txt ...
creating /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/ab_initio_parameters/augustus/species/plecoglossus_altivelis/plecoglossus_altivelis_metapars.cfg ...
The necessary files for training plecoglossus_altivelis have been created.
Now, either run etraining or optimize_parameters.pl with --species=plecoglossus_altivelis.
etraining quickly estimates the parameters from a file with training genes.
optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters.

# Read in 2609 genbank sequences.
Quantiles of the GC contents in the training set:
0%	0.345
5%	0.39	10%	0.403
15%	0.41	20%	0.417
25%	0.423	30%	0.43
35%	0.435	40%	0.441
45%	0.447	50%	0.452
55%	0.457	60%	0.462
65%	0.469	70%	0.475
75%	0.481	80%	0.488
85%	0.494	90%	0.505
95%	0.522	100%	0.599
HMM-training the parameters...
i= 0 bc= (0.237, 0.263, 0.263, 0.237)
 ** building model for exons *EXON*
gene g_2124-T1 transcr. 1 in sequence scaffold_5_10971320-10975667: Initial exon has length < 3!
gene g_2232-T1 transcr. 1 in sequence scaffold_6_5190112-5199009: Initial exon has length < 3!
gene g_386-T1 transcr. 1 in sequence scaffold_12_144203-148194: Initial exon has length < 3!
gene g_397-T1 transcr. 1 in sequence scaffold_12_3397687-3400889: Terminal exon doesn't end in stop codon. Variable stopCodonExcludedFromCDS set right?
gene g_604-T1 transcr. 1 in sequence scaffold_13_13973327-13976069: Initial exon has length < 3!
gene g_676-T1 transcr. 1 in sequence scaffold_14_8498411-8501864: Initial exon has length < 3!
gene g_1049-T1 transcr. 1 in sequence scaffold_18_7021203-7023695: Initial exon has length < 3!
gene g_1084-T1 transcr. 1 in sequence scaffold_19_608874-615357: Initial exon has length < 3!
gene g_1308-T1 transcr. 1 in sequence scaffold_20_1572610-1576180: Initial exon has length < 3!
gene g_1401-T1 transcr. 1 in sequence scaffold_21_5545083-5550221: Terminal exon doesn't end in stop codon. Variable stopCodonExcludedFromCDS set right?
gene g_1604-T1 transcr. 1 in sequence scaffold_24_8118201-8122401: Terminal exon doesn't end in stop codon. Variable stopCodonExcludedFromCDS set right?
start codon frequencies: ATG(2601)
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
 number of bases in the reading frames: 914392 916899 916908
--- frame = 0 ---    minPatSum = 233
--- frame = 1 ---    minPatSum = 233
--- frame = 2 ---    minPatSum = 233
--- initial frame = 0 ---    minPatSum = 233
--- initial frame = 1 ---    minPatSum = 233
--- initial frame = 2 ---    minPatSum = 233
--- internal exon terminal frame = 0 ---    minPatSum = 233
--- internal exon terminal frame = 1 ---    minPatSum = 233
--- internal exon terminal frame = 2 ---    minPatSum = 233
single, initial, internal, terminal mean exon lengths :
n.a.	143	131	194
single exon : 0
initial exon 0 : 1138
initial exon 1 : 917
initial exon 2 : 546
internal exon 0 : 7314
internal exon 1 : 4401
internal exon 2 : 3506
terminal exon : 2606
Frequency of stop codons:
tag:  639 (0.245)
taa:  692 (0.266)
tga: 1275 (0.489)
end *EXON*
Storing parameters to file...
Writing exon model parameters [1] to file /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/ab_initio_parameters/augustus/species/plecoglossus_altivelis/plecoglossus_altivelis_exon_probs.pbl.