-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_19367329-19545588

-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_5-snap.3664-T1
Couldn't classify 57901, 58089
Couldn't classify 58791, 58914
Sorry, prediction pasa_asmbl_45092.p2 fails validation.
(TTG)	 GG	57901-58089	GT	TGG
(ACT)	 AG	58459-58514	GT	AAG
(GTA)	 AG	58791-58914	CA	GCC
-recovered pasa_asmbl_45092.p2, internal, 58459, 58514
Valid prediction for GeneMark_model.23642_t
Valid prediction for snap_scaffold_5-snap.3665-T1
Valid prediction for GlimmerHMM_glimmerT_14154-T1
Valid prediction for GeneMark_model.23632_t
Valid prediction for Augustus_model.g9463.t1
Valid prediction for snap_scaffold_5-snap.3668-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3670-T1
Valid prediction for GlimmerHMM_glimmerT_14161-T1
Valid prediction for snap_scaffold_5-snap.3669-T1
Valid prediction for Augustus_model.g9460.t1
Valid prediction for snap_scaffold_5-snap.3678-T1
Valid prediction for GlimmerHMM_glimmerT_14145-T1
Valid prediction for Augustus_model.g9467.t1
Valid prediction for snap_scaffold_5-snap.3679-T1
Valid prediction for snap_scaffold_5-snap.3681-T1
Valid prediction for GlimmerHMM_glimmerT_14140-T1
Valid prediction for GeneMark_model.23639_t
Valid prediction for GlimmerHMM_glimmerT_14156-T1
Couldn't classify 71939, 72036
Sorry, prediction pasa_asmbl_44972.p1 fails validation.
(ACT)	 CC	71939-72036	GT	AGG
(GGG)	 AG	72152-72384	GT	TGG
(AGA)	 AG	72620-73201	GT	AGG
(AGG)	 AG	73398-73600	TC	AAT
-recovered pasa_asmbl_44972.p1, terminal, 73398, 73600
-recovered pasa_asmbl_44972.p1, internal, 72152, 72384
-recovered pasa_asmbl_44972.p1, internal, 72620, 73201
Valid prediction for snap_scaffold_5-snap.3680-T1
Valid prediction for GlimmerHMM_glimmerT_14149-T1
Valid prediction for Augustus_model.g9459.t1
Valid prediction for GeneMark_model.23648_t
Valid prediction for snap_scaffold_5-snap.3666-T1
Valid prediction for Augustus_model.g9461.t1
Valid prediction for GeneMark_model.23640_t
Valid prediction for snap_scaffold_5-snap.3661-T1
Valid prediction for GlimmerHMM_glimmerT_14147-T1
Valid prediction for Augustus_model.g9457.t1
Valid prediction for Augustus_model.g9469.t1
Valid prediction for snap_scaffold_5-snap.3663-T1
Valid prediction for GlimmerHMM_glimmerT_14151-T1
Valid prediction for GlimmerHMM_glimmerT_14144-T1
Valid prediction for GeneMark_model.23635_t

-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.g9468.t1
Valid prediction for GlimmerHMM_glimmerT_14157-T1
Valid prediction for GeneMark_model.23645_t
Valid prediction for GeneMark_model.23633_t
Valid prediction for snap_scaffold_5-snap.3659-T1
Valid prediction for GlimmerHMM_glimmerT_14148-T1
Valid prediction for snap_scaffold_5-snap.3658-T1
Valid prediction for snap_scaffold_5-snap.3657-T1
Valid prediction for pasa_asmbl_46289.p1
Valid prediction for GlimmerHMM_glimmerT_14152-T1
Valid prediction for snap_scaffold_5-snap.3675-T1
Valid prediction for GeneMark_model.23643_t
Valid prediction for Augustus_model.g9455.t1
Valid prediction for Augustus_model.g9456.t1
Valid prediction for GeneMark_model.23636_t
Valid prediction for GeneMark_model.23646_t
Valid prediction for GlimmerHMM_glimmerT_14162-T1
Valid prediction for snap_scaffold_5-snap.3660-T1
Valid prediction for snap_scaffold_5-snap.3671-T1
Valid prediction for GlimmerHMM_glimmerT_14137-T1
Valid prediction for HiQ_model.g9464.t1
Valid prediction for HiQ_model.g9452.t1
Valid prediction for GlimmerHMM_glimmerT_14143-T1
Valid prediction for Augustus_model.g9470.t1
Valid prediction for GlimmerHMM_glimmerT_14155-T1
Valid prediction for snap_scaffold_5-snap.3672-T1
Valid prediction for Augustus_model.g9471.t1
Valid prediction for GlimmerHMM_glimmerT_14153-T1
Valid prediction for snap_scaffold_5-snap.3677-T1
Valid prediction for GeneMark_model.23634_t
Valid prediction for pasa_asmbl_46281.p1
Valid prediction for snap_scaffold_5-snap.3656-T1
Valid prediction for GeneMark_model.23644_t
Valid prediction for GeneMark_model.23641_t
Valid prediction for GlimmerHMM_glimmerT_14138-T1
Valid prediction for Augustus_model.g9472.t1
Valid prediction for GlimmerHMM_glimmerT_14150-T1
Valid prediction for Augustus_model.g9454.t1
Valid prediction for snap_scaffold_5-snap.3674-T1
Valid prediction for snap_scaffold_5-snap.3673-T1
Couldn't classify 64885, 65301
Sorry, prediction pasa_asmbl_44975.p1 fails validation.
(GGC)	 CT	64885-65301	AA	TAA
Couldn't classify 153737, 153885
Sorry, prediction pasa_asmbl_46287.p1 fails validation.
(ATG)	 AC	152853-152913	GT	AGG
(GTT)	 AG	153009-153187	GT	GAG
(GGG)	 AG	153289-153392	GT	TGG
(GTG)	 AG	153498-153613	GT	AAG
(AAG)	 AG	153737-153885	GG	AGG
-recovered pasa_asmbl_46287.p1, initial, 152853, 152913
-recovered pasa_asmbl_46287.p1, internal, 153009, 153187
-recovered pasa_asmbl_46287.p1, internal, 153289, 153392
-recovered pasa_asmbl_46287.p1, internal, 153498, 153613
Valid prediction for GlimmerHMM_glimmerT_14142-T1
Valid prediction for Augustus_model.g9465.t1
Valid prediction for GlimmerHMM_glimmerT_14141-T1
Valid prediction for GlimmerHMM_glimmerT_14159-T1
Valid prediction for GeneMark_model.23638_t
Valid prediction for Augustus_model.g9473.t1
Valid prediction for GlimmerHMM_glimmerT_14158-T1
Valid prediction for Augustus_model.g9458.t1
Valid prediction for GlimmerHMM_glimmerT_14146-T1
Valid prediction for Augustus_model.g9453.t1
Valid prediction for snap_scaffold_5-snap.3667-T1
Couldn't classify 165429, 165857
Sorry, prediction pasa_asmbl_45103.p1 fails validation.
(GCA)	 GC	165429-165857	AA	TCA
Valid prediction for GlimmerHMM_glimmerT_14160-T1
Valid prediction for Augustus_model.g9462.t1
Valid prediction for snap_scaffold_5-snap.3676-T1
Valid prediction for GeneMark_model.23631_t
Valid prediction for snap_scaffold_5-snap.3682-T1
Valid prediction for snap_scaffold_5-snap.3662-T1
Valid prediction for GlimmerHMM_glimmerT_14139-T1
Valid prediction for GlimmerHMM_glimmerT_14136-T1
Valid prediction for Augustus_model.g9466.t1

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

-building trellis in range 1 - 178260
-exon list size: 303


building trellis

0.3    
0.7    
1.0    
1.3    
1.6    
2.0    
2.3    
2.6    
3.0    
3.3    
3.6    
3.9    
4.3    
4.6    
4.9    
5.2    
5.6    
5.9    
6.2    
6.6    
6.9    
7.2    
7.5    
7.9    
8.2    
8.5    
8.9    
9.2    
9.5    
9.8    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.5    
12.8    
13.1    
13.4    
13.8    
14.1    
14.4    
14.8    
15.1    
15.4    
15.7    
16.1    
16.4    
16.7    
17.0    
17.4    
17.7    
18.0    
18.4    
18.7    
19.0    
19.3    
19.7    
20.0    
20.3    
20.7    
21.0    
21.3    
21.6    
22.0    
22.3    
22.6    
23.0    
23.3    
23.6    
23.9    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.6    
26.9    
27.2    
27.5    
27.9    
28.2    
28.5    
28.9    
29.2    
29.5    
29.8    
30.2    
30.5    
30.8    
31.1    
31.5    
31.8    
32.1    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.8    
35.1    
35.4    
35.7    
36.1    
36.4    
36.7    
37.0    
37.4    
37.7    
38.0    
38.4    
38.7    
39.0    
39.3    
39.7    
40.0    
40.3    
40.7    
41.0    
41.3    
41.6    
42.0    
42.3    
42.6    
43.0    
43.3    
43.6    
43.9    
44.3    
44.6    
44.9    
45.2    
45.6    
45.9    
46.2    
46.6    
46.9    
47.2    
47.5    
47.9    
48.2    
48.5    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.5    
51.8    
52.1    
52.5    
52.8    
53.1    
53.4    
53.8    
54.1    
54.4    
54.8    
55.1    
55.4    
55.7    
56.1    
56.4    
56.7    
57.0    
57.4    
57.7    
58.0    
58.4    
58.7    
59.0    
59.3    
59.7    
60.0    
60.3    
60.7    
61.0    
61.3    
61.6    
62.0    
62.3    
62.6    
63.0    
63.3    
63.6    
63.9    
64.3    
64.6    
64.9    
65.2    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.9    
68.2    
68.5    
68.9    
69.2    
69.5    
69.8    
70.2    
70.5    
70.8    
71.1    
71.5    
71.8    
72.1    
72.5    
72.8    
73.1    
73.4    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.1    
76.4    
76.7    
77.0    
77.4    
77.7    
78.0    
78.4    
78.7    
79.0    
79.3    
79.7    
80.0    
80.3    
80.7    
81.0    
81.3    
81.6    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.3    
84.6    
84.9    
85.2    
85.6    
85.9    
86.2    
86.6    
86.9    
87.2    
87.5    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.1    
91.5    
91.8    
92.1    
92.5    
92.8    
93.1    
93.4    
93.8    
94.1    
94.4    
94.8    
95.1    
95.4    
95.7    
96.1    
96.4    
96.7    
97.0    
97.4    
97.7    
98.0    
98.4    
98.7    
99.0    
99.3    
99.7    
-found 27 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 162791 - 178260
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support