Will create parameters for a EUKARYOTIC species!
creating directory /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/ab_initio_parameters/augustus/species/species_name/ ...
creating /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/ab_initio_parameters/augustus/species/species_name/species_name_parameters.cfg ...
creating /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/ab_initio_parameters/augustus/species/species_name/species_name_weightmatrix.txt ...
creating /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/ab_initio_parameters/augustus/species/species_name/species_name_metapars.cfg ...
The necessary files for training species_name have been created.
Now, either run etraining or optimize_parameters.pl with --species=species_name.
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 2751 genbank sequences.
Quantiles of the GC contents in the training set:
0%	0.345
5%	0.391	10%	0.404
15%	0.411	20%	0.418
25%	0.425	30%	0.43
35%	0.436	40%	0.443
45%	0.448	50%	0.454
55%	0.459	60%	0.465
65%	0.472	70%	0.477
75%	0.483	80%	0.49
85%	0.498	90%	0.509
95%	0.525	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_2249-T1 transcr. 1 in sequence scaffold_5_10971320-10975667: Initial exon has length < 3!
gene g_2352-T1 transcr. 1 in sequence scaffold_6_5190112-5199009: Initial exon has length < 3!
gene g_2707-T1 transcr. 1 in sequence scaffold_9_9718344-9724495: Terminal exon doesn't end in stop codon. Variable stopCodonExcludedFromCDS set right?
gene g_186-T1 transcr. 1 in sequence scaffold_10_3076472-3080908: Initial exon has length < 3!
gene g_411-T1 transcr. 1 in sequence scaffold_12_144203-148194: Initial exon has length < 3!
gene g_420-T1 transcr. 1 in sequence scaffold_12_3397687-3400889: Terminal exon doesn't end in stop codon. Variable stopCodonExcludedFromCDS set right?
gene g_642-T1 transcr. 1 in sequence scaffold_13_13973327-13976069: Initial exon has length < 3!
gene g_1117-T1 transcr. 1 in sequence scaffold_18_7021203-7023695: Initial exon has length < 3!
gene g_1161-T1 transcr. 1 in sequence scaffold_19_608874-615357: Initial exon has length < 3!
gene g_1389-T1 transcr. 1 in sequence scaffold_20_1572610-1576180: Initial exon has length < 3!
gene g_1485-T1 transcr. 1 in sequence scaffold_21_5545083-5550221: Terminal exon doesn't end in stop codon. Variable stopCodonExcludedFromCDS set right?
gene g_1695-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(2743)
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
 number of bases in the reading frames: 995241 997894 997900
--- 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.	142	132	195
single exon : 0
initial exon 0 : 1215
initial exon 1 : 961
initial exon 2 : 567
internal exon 0 : 7912
internal exon 1 : 4814
internal exon 2 : 3737
terminal exon : 2747
Frequency of stop codons:
tag:  663 (0.241)
taa:  715 (0.26)
tga: 1369 (0.498)
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/test/fun/predict_misc/ab_initio_parameters/augustus/species/species_name/species_name_exon_probs.pbl.