-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_475

-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 GeneMark_model.107733_t
Couldn't classify 1177, 1270
Sorry, prediction snap_scaffold_475-snap.1-T1 fails validation.
(AGA)	 AG	1177-1270	GT	GGG
(GGC)	 AG	2415-2634	GT	GGG
(GAT)	 AG	3015-3084	TT	GAT
-recovered snap_scaffold_475-snap.1-T1, terminal, 3015, 3084
-recovered snap_scaffold_475-snap.1-T1, internal, 1177, 1270
-recovered snap_scaffold_475-snap.1-T1, internal, 2415, 2634
Couldn't classify 164, 330
Sorry, prediction GeneMark_model.107730_t fails validation.
(ATC)	 AG	164-330	GT	TGG
(GGG)	 AG	365-468	GT	TGG
(GGG)	 AG	526-606	GT	TGG
(GGG)	 AG	775-786	GT	TGG
(GGG)	 AG	821-832	GT	TGG
(GGG)	 AG	867-878	GT	TGG
(GGG)	 AG	913-1022	GT	GAG
(AAG)	 AG	1106-1135	GT	AGG
(AGG)	 AG	1196-1270	GT	GGG
(GAT)	 AG	1426-1495	GT	CTG
(GCC)	 AG	1526-1563	GT	CTG
(CTC)	 AG	1650-1665	GT	CTG
(CTG)	 AG	1713-1733	GT	CTG
(TCC)	 AG	1759-1767	GT	CTG
(GGC)	 AG	1806-1859	GT	GAG
-recovered GeneMark_model.107730_t, terminal, 1806, 1859
-recovered GeneMark_model.107730_t, internal, 164, 330
-recovered GeneMark_model.107730_t, internal, 365, 468
-recovered GeneMark_model.107730_t, internal, 526, 606
-recovered GeneMark_model.107730_t, internal, 775, 786
-recovered GeneMark_model.107730_t, internal, 821, 832
-recovered GeneMark_model.107730_t, internal, 867, 878
-recovered GeneMark_model.107730_t, internal, 913, 1022
-recovered GeneMark_model.107730_t, internal, 1106, 1135
-recovered GeneMark_model.107730_t, internal, 1196, 1270
-recovered GeneMark_model.107730_t, internal, 1426, 1495
-recovered GeneMark_model.107730_t, internal, 1526, 1563
-recovered GeneMark_model.107730_t, internal, 1650, 1665
-recovered GeneMark_model.107730_t, internal, 1713, 1733
-recovered GeneMark_model.107730_t, internal, 1759, 1767
-recovered GeneMark_model.107730_t, internal, 1806, 1859

-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_61894-T1
Valid prediction for GeneMark_model.107731_t
Valid prediction for CodingQuarry_transcript_49358-T1
Valid prediction for GlimmerHMM_glimmerT_61893-T1
Couldn't classify 23, 188
Sorry, prediction GeneMark_model.107734_t fails validation.
(GCC)	 AG	23-188	GT	AGG
(AAC)	 AG	521-544	CT	GAC
-recovered GeneMark_model.107734_t, terminal, 521, 544
-recovered GeneMark_model.107734_t, internal, 23, 188
Valid prediction for Augustus_model.g41143.t1
Couldn't classify 23, 188
Sorry, prediction snap_scaffold_475-snap.2-T1 fails validation.
(GCC)	 AG	23-188	GT	AGG
(AAT)	 AG	1168-1216	GT	AGG
(GTC)	 AG	1809-2104	GA	AGG
-recovered snap_scaffold_475-snap.2-T1, terminal, 1809, 2104
-recovered snap_scaffold_475-snap.2-T1, internal, 23, 188
-recovered snap_scaffold_475-snap.2-T1, internal, 1168, 1216

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

-building trellis in range 1 - 6672
-exon list size: 50


building trellis

1.9    
3.8    
5.8    
7.7    
9.6    
11.5    
13.5    
15.4    
17.3    
19.2    
21.2    
23.1    
25.0    
26.9    
28.8    
30.8    
32.7    
34.6    
36.5    
38.5    
40.4    
42.3    
44.2    
46.2    
48.1    
50.0    
51.9    
53.8    
55.8    
57.7    
59.6    
61.5    
63.5    
65.4    
67.3    
69.2    
71.2    
73.1    
75.0    
76.9    
78.8    
80.8    
82.7    
84.6    
86.5    
88.5    
90.4    
92.3    
94.2    
96.2    
98.1    
-found 2 predictions from path traversal

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