-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_166

-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_166-snap.5-T1
Couldn't classify 11300, 11444
Sorry, prediction GeneMark_model.106807_t fails validation.
(ATG)	 CC	6979-7150	GT	AGG
(GGA)	 AG	7196-7350	GT	ACG
(GGC)	 AG	7428-7615	GT	ATG
(GAC)	 AG	7654-8519	GT	CTG
(GTA)	 AG	8540-8606	GT	GGG
(GCA)	 AG	8853-9215	GT	AGG
(CGC)	 AG	9282-9635	GT	GGG
(TAG)	 AG	9657-9674	GT	GCG
(GCA)	 AG	9702-9797	GT	AGG
(GGA)	 AG	9835-9882	GT	GGG
(AGT)	 AG	9975-10067	GT	CCG
(AAG)	 AG	10098-10287	GT	AGG
(GAT)	 AG	10352-10383	GT	GGG
(GAC)	 AG	10404-10628	GT	GGG
(AGA)	 AG	10660-10812	GT	CAG
(GGA)	 AG	10842-10994	GT	GAG
(AAG)	 AG	11026-11058	GT	GGG
(GAG)	 AG	11083-11121	GT	AAG
(AGC)	 AG	11149-11274	GC	AAG
(GAA)	 AG	11300-11444	GT	AAG
-recovered GeneMark_model.106807_t, initial, 6979, 7150
-recovered GeneMark_model.106807_t, internal, 7196, 7350
-recovered GeneMark_model.106807_t, internal, 7428, 7615
-recovered GeneMark_model.106807_t, internal, 7654, 8519
-recovered GeneMark_model.106807_t, internal, 8540, 8606
-recovered GeneMark_model.106807_t, internal, 8853, 9215
-recovered GeneMark_model.106807_t, internal, 9282, 9635
-recovered GeneMark_model.106807_t, internal, 9657, 9674
-recovered GeneMark_model.106807_t, internal, 9702, 9797
-recovered GeneMark_model.106807_t, internal, 9835, 9882
-recovered GeneMark_model.106807_t, internal, 9975, 10067
-recovered GeneMark_model.106807_t, internal, 10098, 10287
-recovered GeneMark_model.106807_t, internal, 10352, 10383
-recovered GeneMark_model.106807_t, internal, 10404, 10628
-recovered GeneMark_model.106807_t, internal, 10660, 10812
-recovered GeneMark_model.106807_t, internal, 10842, 10994
-recovered GeneMark_model.106807_t, internal, 11026, 11058
-recovered GeneMark_model.106807_t, internal, 11083, 11121
-recovered GeneMark_model.106807_t, internal, 11149, 11274
-recovered GeneMark_model.106807_t, internal, 11300, 11444
Valid prediction for snap_scaffold_166-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_61433-T1
Valid prediction for Augustus_model.g40857.t1
Valid prediction for GeneMark_model.106805_t
Valid prediction for snap_scaffold_166-snap.6-T1
Couldn't classify 259, 312
Sorry, prediction GeneMark_model.106804_t fails validation.
(AGA)	 AG	259-312	GT	ATG
(GTG)	 AG	386-436	GT	AGG
(GGG)	 AG	468-512	GT	AGG
(AAG)	 AG	536-580	GT	AGG
(GAG)	 AG	604-615	GT	GGG
(GGG)	 AG	711-719	GT	AAG
(ACA)	 AG	1359-1404	AC	AGA
-recovered GeneMark_model.106804_t, terminal, 1359, 1404
-recovered GeneMark_model.106804_t, internal, 259, 312
-recovered GeneMark_model.106804_t, internal, 386, 436
-recovered GeneMark_model.106804_t, internal, 468, 512
-recovered GeneMark_model.106804_t, internal, 536, 580
-recovered GeneMark_model.106804_t, internal, 604, 615
-recovered GeneMark_model.106804_t, internal, 711, 719
Valid prediction for snap_scaffold_166-snap.3-T1
Valid prediction for Augustus_model.g40856.t1
Valid prediction for GlimmerHMM_glimmerT_61434-T1
Valid prediction for snap_scaffold_166-snap.1-T1
Valid prediction for snap_scaffold_166-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_61435-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 Augustus_model.g40855.t1
Valid prediction for GeneMark_model.106806_t

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

-building trellis in range 1 - 11632
-exon list size: 85


building trellis

1.1    
2.3    
3.4    
4.6    
5.7    
6.9    
8.0    
9.2    
10.3    
11.5    
12.6    
13.8    
14.9    
16.1    
17.2    
18.4    
19.5    
20.7    
21.8    
23.0    
24.1    
25.3    
26.4    
27.6    
28.7    
29.9    
31.0    
32.2    
33.3    
34.5    
35.6    
36.8    
37.9    
39.1    
40.2    
41.4    
42.5    
43.7    
44.8    
46.0    
47.1    
48.3    
49.4    
50.6    
51.7    
52.9    
54.0    
55.2    
56.3    
57.5    
58.6    
59.8    
60.9    
62.1    
63.2    
64.4    
65.5    
66.7    
67.8    
69.0    
70.1    
71.3    
72.4    
73.6    
74.7    
75.9    
77.0    
78.2    
79.3    
80.5    
81.6    
82.8    
83.9    
85.1    
86.2    
87.4    
88.5    
89.7    
90.8    
92.0    
93.1    
94.3    
95.4    
96.6    
97.7    
98.9    
-found 5 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 4 predictions persist after filtering for low support