-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_4232615-4346661

-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_28-snap.1010-T1
Valid prediction for CodingQuarry_transcript_43534-T1
Valid prediction for snap_scaffold_28-snap.1015-T1
Valid prediction for HiQ_model.g39976.t1
Valid prediction for GlimmerHMM_glimmerT_60058-T1
Valid prediction for snap_scaffold_28-snap.1007-T1
Valid prediction for GeneMark_model.104687_t
Valid prediction for GeneMark_model.104683_t
Valid prediction for GeneMark_model.104690_t
Valid prediction for GeneMark_model.104684_t
Valid prediction for snap_scaffold_28-snap.1018-T1
Valid prediction for GlimmerHMM_glimmerT_60052-T1
Valid prediction for snap_scaffold_28-snap.1009-T1
Valid prediction for GeneMark_model.104675_t
Valid prediction for snap_scaffold_28-snap.1008-T1
Couldn't classify 12871, 12978
Couldn't classify 15427, 15534
Sorry, prediction pasa_asmbl_38225.p1 fails validation.
(GGT)	 AG	12871-12978	GT	TGG
(GGA)	 AG	13069-13122	GT	AGG
(GGT)	 AG	13370-13423	GT	AGG
(GGT)	 AG	14009-14065	GT	GAG
(GGT)	 AG	14302-14355	GT	AGG
(GGT)	 AG	14501-14554	GT	CTG
(GGA)	 AG	14647-14700	GT	AAG
(GGT)	 AG	14795-14848	GT	CAG
(GGT)	 AG	15014-15121	GT	AGG
(GGG)	 AG	15232-15339	GT	AGG
(GGG)	 AG	15427-15534	GT	TGG
-recovered pasa_asmbl_38225.p1, internal, 12871, 12978
-recovered pasa_asmbl_38225.p1, internal, 13069, 13122
-recovered pasa_asmbl_38225.p1, internal, 13370, 13423
-recovered pasa_asmbl_38225.p1, internal, 14009, 14065
-recovered pasa_asmbl_38225.p1, internal, 14302, 14355
-recovered pasa_asmbl_38225.p1, internal, 14501, 14554
-recovered pasa_asmbl_38225.p1, internal, 14647, 14700
-recovered pasa_asmbl_38225.p1, internal, 14795, 14848
-recovered pasa_asmbl_38225.p1, internal, 15014, 15121
-recovered pasa_asmbl_38225.p1, internal, 15232, 15339
-recovered pasa_asmbl_38225.p1, internal, 15427, 15534
Valid prediction for GlimmerHMM_glimmerT_60054-T1
Valid prediction for Augustus_model.g39981.t1
Valid prediction for GeneMark_model.104681_t
Valid prediction for snap_scaffold_28-snap.1024-T1
Valid prediction for snap_scaffold_28-snap.1014-T1
Valid prediction for GlimmerHMM_glimmerT_60047-T1
Valid prediction for Augustus_model.g39979.t1
Valid prediction for GlimmerHMM_glimmerT_60061-T1
Valid prediction for GlimmerHMM_glimmerT_60059-T1
Valid prediction for CodingQuarry_transcript_43536-T1
Valid prediction for CodingQuarry_transcript_43535-T1
Valid prediction for GlimmerHMM_glimmerT_60048-T1
Valid prediction for GlimmerHMM_glimmerT_60062-T1
Valid prediction for GlimmerHMM_glimmerT_60055-T1
Valid prediction for Augustus_model.g39977.t1
Valid prediction for GeneMark_model.104676_t
Valid prediction for GeneMark_model.104680_t
Valid prediction for snap_scaffold_28-snap.1021-T1
Valid prediction for Augustus_model.g39984.t1
Valid prediction for pasa_asmbl_38227.p1
Valid prediction for CodingQuarry_transcript_43539-T1
Valid prediction for GlimmerHMM_glimmerT_60063-T1
Valid prediction for GlimmerHMM_glimmerT_60049-T1
Valid prediction for pasa_asmbl_38554.p1
Valid prediction for GeneMark_model.104679_t
Valid prediction for Augustus_model.g39982.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 snap_scaffold_28-snap.1023-T1
Valid prediction for Augustus_model.g39978.t1
Valid prediction for GlimmerHMM_glimmerT_60057-T1
Valid prediction for snap_scaffold_28-snap.1012-T1
Valid prediction for HiQ_model.g39973.t1
Valid prediction for GlimmerHMM_glimmerT_60051-T1
Valid prediction for CodingQuarry_transcript_43538-T1
Valid prediction for CodingQuarry_transcript_43537-T1
Valid prediction for GlimmerHMM_glimmerT_60056-T1
Valid prediction for GeneMark_model.104689_t
Couldn't classify 88739, 88771
Sorry, prediction pasa_asmbl_37526.p1 fails validation.
(CAC)	 CG	88739-88771	GT	TGG
(GCA)	 AG	88989-89063	GT	AAG
(AAC)	 AG	89241-89334	GT	AGG
(GCA)	 AG	89540-89607	GT	AGG
(CAT)	 AG	89706-89824	GT	AAG
(GAT)	 AG	89916-90042	AC	AGA
-recovered pasa_asmbl_37526.p1, terminal, 89916, 90042
-recovered pasa_asmbl_37526.p1, internal, 88989, 89063
-recovered pasa_asmbl_37526.p1, internal, 89241, 89334
-recovered pasa_asmbl_37526.p1, internal, 89540, 89607
-recovered pasa_asmbl_37526.p1, internal, 89706, 89824
Valid prediction for GeneMark_model.104691_t
Valid prediction for snap_scaffold_28-snap.1019-T1
Valid prediction for Augustus_model.g39983.t1
Valid prediction for GeneMark_model.104685_t
Valid prediction for GeneMark_model.104686_t
Couldn't classify 84446, 85177
Sorry, prediction pasa_asmbl_37528.p1 fails validation.
(CTG)	 GG	84446-85177	GT	GAG
(ATC)	 AG	85423-85707	GG	GAG
-recovered pasa_asmbl_37528.p1, terminal, 85423, 85707
Valid prediction for GeneMark_model.104688_t
Valid prediction for GeneMark_model.104678_t
Valid prediction for HiQ_model.g39974.t1
Valid prediction for GeneMark_model.104677_t
Valid prediction for snap_scaffold_28-snap.1011-T1
Valid prediction for snap_scaffold_28-snap.1022-T1
Valid prediction for snap_scaffold_28-snap.1013-T1
Valid prediction for GlimmerHMM_glimmerT_60060-T1
Valid prediction for Augustus_model.g39980.t1
Valid prediction for pasa_asmbl_37524.p1
Valid prediction for snap_scaffold_28-snap.1016-T1
Valid prediction for GeneMark_model.104682_t
Valid prediction for snap_scaffold_28-snap.1017-T1
Valid prediction for snap_scaffold_28-snap.1020-T1
Valid prediction for HiQ_model.g39975.t1
Valid prediction for GlimmerHMM_glimmerT_60053-T1
Valid prediction for GlimmerHMM_glimmerT_60050-T1

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

-building trellis in range 1 - 114047
-exon list size: 301


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.6    
3.0    
3.3    
3.6    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
5.9    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.3    
8.6    
8.9    
9.2    
9.6    
9.9    
10.2    
10.6    
10.9    
11.2    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.9    
14.2    
14.5    
14.9    
15.2    
15.5    
15.8    
16.2    
16.5    
16.8    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.5    
19.8    
20.1    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.8    
23.1    
23.4    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.1    
26.4    
26.7    
27.1    
27.4    
27.7    
28.1    
28.4    
28.7    
29.0    
29.4    
29.7    
30.0    
30.4    
30.7    
31.0    
31.4    
31.7    
32.0    
32.3    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
37.0    
37.3    
37.6    
38.0    
38.3    
38.6    
38.9    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.3    
41.6    
41.9    
42.2    
42.6    
42.9    
43.2    
43.6    
43.9    
44.2    
44.6    
44.9    
45.2    
45.5    
45.9    
46.2    
46.5    
46.9    
47.2    
47.5    
47.9    
48.2    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.8    
52.1    
52.5    
52.8    
53.1    
53.5    
53.8    
54.1    
54.5    
54.8    
55.1    
55.4    
55.8    
56.1    
56.4    
56.8    
57.1    
57.4    
57.8    
58.1    
58.4    
58.7    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.1    
61.4    
61.7    
62.0    
62.4    
62.7    
63.0    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.7    
68.0    
68.3    
68.6    
69.0    
69.3    
69.6    
70.0    
70.3    
70.6    
71.0    
71.3    
71.6    
71.9    
72.3    
72.6    
72.9    
73.3    
73.6    
73.9    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.6    
76.9    
77.2    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.9    
80.2    
80.5    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.2    
83.5    
83.8    
84.2    
84.5    
84.8    
85.1    
85.5    
85.8    
86.1    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.8    
89.1    
89.4    
89.8    
90.1    
90.4    
90.8    
91.1    
91.4    
91.7    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.1    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.4    
96.7    
97.0    
97.4    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 18 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support