-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_158

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GlimmerHMM_glimmerT_61418-T1
Couldn't classify 271, 418
Sorry, prediction Augustus_model.g40848.t1 fails validation.
(GTC)	 AG	271-418	GT	ATG
(TCG)	 AG	607-678	GT	ATG
(AGA)	 AG	1070-1141	GT	CTG
(TGT)	 AG	1901-1976	GT	AAG
-recovered Augustus_model.g40848.t1, terminal, 1901, 1976
-recovered Augustus_model.g40848.t1, internal, 271, 418
-recovered Augustus_model.g40848.t1, internal, 607, 678
-recovered Augustus_model.g40848.t1, internal, 1070, 1141
-recovered Augustus_model.g40848.t1, internal, 1901, 1976
Valid prediction for GeneMark_model.106776_t
Couldn't classify 66, 95
Sorry, prediction GeneMark_model.106774_t fails validation.
(TGT)	 AG	66-95	GT	GGG
(TGT)	 AG	118-129	GT	TGG
(GTC)	 AG	155-172	GT	AGG
(GAA)	 AG	196-239	GT	AGG
(GTC)	 AG	271-418	GT	ATG
(TCG)	 AG	607-678	GT	ATG
(AGA)	 AG	1070-1141	GT	CTG
(TGT)	 AG	1901-1976	GT	AAG
-recovered GeneMark_model.106774_t, terminal, 1901, 1976
-recovered GeneMark_model.106774_t, internal, 66, 95
-recovered GeneMark_model.106774_t, internal, 118, 129
-recovered GeneMark_model.106774_t, internal, 155, 172
-recovered GeneMark_model.106774_t, internal, 196, 239
-recovered GeneMark_model.106774_t, internal, 271, 418
-recovered GeneMark_model.106774_t, internal, 607, 678
-recovered GeneMark_model.106774_t, internal, 1070, 1141
-recovered GeneMark_model.106774_t, internal, 1901, 1976
Valid prediction for Augustus_model.g40849.t1
Couldn't classify 11236, 11274
Sorry, prediction snap_scaffold_158-snap.2-T1 fails validation.
(ATG)	 TG	3456-3460	GT	TTG
(AGT)	 AG	5691-5721	GT	AGG
(TTC)	 AG	6398-6514	GT	TGG
(TGC)	 AG	6821-7035	GT	AGG
(CCC)	 AG	7335-7489	GT	AGG
(GTC)	 AG	8087-8271	GT	GCG
(GAT)	 AG	8331-8945	GT	AGG
(TCT)	 AG	9029-9185	GT	CGG
(AGG)	 AG	9470-9600	GT	AGG
(AGT)	 AG	11236-11274	GT	ATG
-recovered snap_scaffold_158-snap.2-T1, initial, 3456, 3460
-recovered snap_scaffold_158-snap.2-T1, internal, 5691, 5721
-recovered snap_scaffold_158-snap.2-T1, internal, 6398, 6514
-recovered snap_scaffold_158-snap.2-T1, internal, 6821, 7035
-recovered snap_scaffold_158-snap.2-T1, internal, 7335, 7489
-recovered snap_scaffold_158-snap.2-T1, internal, 8087, 8271
-recovered snap_scaffold_158-snap.2-T1, internal, 8331, 8945
-recovered snap_scaffold_158-snap.2-T1, internal, 9029, 9185
-recovered snap_scaffold_158-snap.2-T1, internal, 9470, 9600
-recovered snap_scaffold_158-snap.2-T1, internal, 11236, 11274
Couldn't classify 9029, 9185
Sorry, prediction GlimmerHMM_glimmerT_61419-T1 fails validation.
(ATG)	 AC	6839-7035	GT	AGG
(CCC)	 AG	7335-7489	GT	AGG
(CTG)	 AG	8362-8945	GT	AGG
(TCT)	 AG	9029-9185	GT	CGG
-recovered GlimmerHMM_glimmerT_61419-T1, initial, 6839, 7035
-recovered GlimmerHMM_glimmerT_61419-T1, internal, 7335, 7489
-recovered GlimmerHMM_glimmerT_61419-T1, internal, 8362, 8945
-recovered GlimmerHMM_glimmerT_61419-T1, internal, 9029, 9185
Couldn't classify 83, 212
Sorry, prediction snap_scaffold_158-snap.1-T1 fails validation.
(AGG)	 AG	83-212	GT	AGG
(GTC)	 AG	271-418	GT	ATG
(TCG)	 AG	607-678	GT	ATG
(AGA)	 AG	1070-1141	GT	CTG
(TGT)	 AG	1901-1972	GT	CTG
(GAC)	 AG	2294-2357	GG	AAG
-recovered snap_scaffold_158-snap.1-T1, terminal, 2294, 2357
-recovered snap_scaffold_158-snap.1-T1, internal, 83, 212
-recovered snap_scaffold_158-snap.1-T1, internal, 271, 418
-recovered snap_scaffold_158-snap.1-T1, internal, 607, 678
-recovered snap_scaffold_158-snap.1-T1, internal, 1070, 1141
-recovered snap_scaffold_158-snap.1-T1, internal, 1901, 1972

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Couldn't classify 221, 288
Sorry, prediction GeneMark_model.106777_t fails validation.
(GAA)	 AG	221-288	GT	GGG
(ATG)	 AG	2518-2683	TG	AGT
-recovered GeneMark_model.106777_t, terminal, 2518, 2683
-recovered GeneMark_model.106777_t, internal, 221, 288
Valid prediction for GeneMark_model.106775_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 11965
-exon list size: 65


building trellis

1.5    
3.0    
4.5    
6.0    
7.5    
9.0    
10.4    
11.9    
13.4    
14.9    
16.4    
17.9    
19.4    
20.9    
22.4    
23.9    
25.4    
26.9    
28.4    
29.9    
31.3    
32.8    
34.3    
35.8    
37.3    
38.8    
40.3    
41.8    
43.3    
44.8    
46.3    
47.8    
49.3    
50.7    
52.2    
53.7    
55.2    
56.7    
58.2    
59.7    
61.2    
62.7    
64.2    
65.7    
67.2    
68.7    
70.1    
71.6    
73.1    
74.6    
76.1    
77.6    
79.1    
80.6    
82.1    
83.6    
85.1    
86.6    
88.1    
89.6    
91.0    
92.5    
94.0    
95.5    
97.0    
98.5    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support