-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_649

-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 snap_scaffold_649-snap.2-T1
Couldn't classify 426, 599
Sorry, prediction Augustus_model.g41269.t1 fails validation.
(GCT)	 AG	426-599	GT	AGG
(ACT)	 AG	1046-1219	GT	AGG
(GCT)	 AG	1425-1595	GT	AGG
(GCT)	 AG	1973-2131	GT	AAG
(TTT)	 AG	2226-2275	GT	GTG
(ACG)	 AG	2702-3273	TG	GAT
-recovered Augustus_model.g41269.t1, terminal, 2702, 3273
-recovered Augustus_model.g41269.t1, internal, 426, 599
-recovered Augustus_model.g41269.t1, internal, 1046, 1219
-recovered Augustus_model.g41269.t1, internal, 1425, 1595
-recovered Augustus_model.g41269.t1, internal, 1973, 2131
-recovered Augustus_model.g41269.t1, internal, 2226, 2275
Couldn't classify 3715, 3985
Sorry, prediction GeneMark_model.108129_t fails validation.
(ATG)	 TC	1666-1668	GT	TGG
(GGC)	 AG	1938-2085	GT	AGG
(ACG)	 AG	2702-2906	GT	ACG
(CAT)	 AG	3129-3269	GT	GAG
(GCT)	 AG	3585-3590	GT	CAG
(CCC)	 AG	3715-3985	GT	CAG
-recovered GeneMark_model.108129_t, initial, 1666, 1668
add_exon() Sorry, GeneMark_model.108129_t 3129-3269-terminal-1 is invalid.
-recovered GeneMark_model.108129_t, terminal, 3129, 3269
-recovered GeneMark_model.108129_t, internal, 1938, 2085
-recovered GeneMark_model.108129_t, internal, 2702, 2906
-recovered GeneMark_model.108129_t, internal, 3129, 3269
-recovered GeneMark_model.108129_t, internal, 3585, 3590
-recovered GeneMark_model.108129_t, internal, 3715, 3985
Valid prediction for snap_scaffold_649-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_62083-T1

-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: -)Valid prediction for GlimmerHMM_glimmerT_62084-T1
Valid prediction for Augustus_model.g41270.t1

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

-building trellis in range 1 - 5153
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 3 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support