-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_19355749-19550329

-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 Augustus_model.g9201.t1
Valid prediction for snap_scaffold_5-snap.3633-T1
Valid prediction for GlimmerHMM_glimmerT_13835-T1
Valid prediction for GlimmerHMM_glimmerT_13833-T1
Valid prediction for GlimmerHMM_glimmerT_13822-T1
Valid prediction for Augustus_model.g9194.t1
Valid prediction for snap_scaffold_5-snap.3637-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3652-T1
Valid prediction for GlimmerHMM_glimmerT_13818-T1
Valid prediction for Augustus_model.g9203.t1
Valid prediction for snap_scaffold_5-snap.3638-T1
Couldn't classify 83519, 83616
Sorry, prediction pasa_asmbl_46319.p1 fails validation.
(ACT)	 CC	83519-83616	GT	AGG
(GGG)	 AG	83732-83964	GT	TGG
(AGA)	 AG	84200-84781	GT	AGG
(AGG)	 AG	84978-85180	TC	AAT
-recovered pasa_asmbl_46319.p1, terminal, 84978, 85180
-recovered pasa_asmbl_46319.p1, internal, 83732, 83964
-recovered pasa_asmbl_46319.p1, internal, 84200, 84781
Valid prediction for snap_scaffold_5-snap.3622-T1
Valid prediction for snap_scaffold_5-snap.3646-T1
Valid prediction for snap_scaffold_5-snap.3648-T1
Valid prediction for GlimmerHMM_glimmerT_13813-T1
Valid prediction for Augustus_model.g9197.t1
Valid prediction for snap_scaffold_5-snap.3630-T1
Valid prediction for Augustus_model.g9193.t1
Valid prediction for snap_scaffold_5-snap.3647-T1
Couldn't classify 69481, 69669
Couldn't classify 70371, 70494
Sorry, prediction pasa_asmbl_46403.p2 fails validation.
(TTG)	 GG	69481-69669	GT	TGG
(ACT)	 AG	70039-70094	GT	AAG
(GTA)	 AG	70371-70494	CA	GCC
-recovered pasa_asmbl_46403.p2, internal, 70039, 70094
Valid prediction for GlimmerHMM_glimmerT_13819-T1
Valid prediction for Augustus_model.g9195.t1
Valid prediction for GlimmerHMM_glimmerT_13845-T1
Valid prediction for GlimmerHMM_glimmerT_13831-T1
Valid prediction for snap_scaffold_5-snap.3635-T1
Valid prediction for snap_scaffold_5-snap.3623-T1
Valid prediction for GlimmerHMM_glimmerT_13825-T1
Valid prediction for snap_scaffold_5-snap.3632-T1
Valid prediction for snap_scaffold_5-snap.3621-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g9185.t1
Valid prediction for GlimmerHMM_glimmerT_13830-T1
Valid prediction for GlimmerHMM_glimmerT_13844-T1
Valid prediction for snap_scaffold_5-snap.3634-T1
Valid prediction for Augustus_model.g9186.t1
Valid prediction for GlimmerHMM_glimmerT_13827-T1
Valid prediction for GlimmerHMM_glimmerT_13843-T1
Valid prediction for snap_scaffold_5-snap.3649-T1
Valid prediction for snap_scaffold_5-snap.3651-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_5-snap.3642-T1
Valid prediction for snap_scaffold_5-snap.3639-T1
Valid prediction for Augustus_model.g9200.t1
Valid prediction for snap_scaffold_5-snap.3645-T1
Valid prediction for Augustus_model.g9204.t1
Valid prediction for GlimmerHMM_glimmerT_13823-T1
Valid prediction for Augustus_model.g9196.t1
Valid prediction for snap_scaffold_5-snap.3625-T1
Valid prediction for GlimmerHMM_glimmerT_13820-T1
Valid prediction for Augustus_model.g9202.t1
Couldn't classify 158478, 158626
Sorry, prediction pasa_asmbl_44912.p1 fails validation.
(ATG)	 AC	157594-157654	GT	AGG
(GTT)	 AG	157750-157928	GT	GAG
(GGG)	 AG	158030-158133	GT	TGG
(GTG)	 AG	158239-158354	GT	AAG
(AAG)	 AG	158478-158626	GG	AGG
-recovered pasa_asmbl_44912.p1, initial, 157594, 157654
-recovered pasa_asmbl_44912.p1, internal, 157750, 157928
-recovered pasa_asmbl_44912.p1, internal, 158030, 158133
-recovered pasa_asmbl_44912.p1, internal, 158239, 158354
Valid prediction for GlimmerHMM_glimmerT_13828-T1
Valid prediction for Augustus_model.g9207.t1
Valid prediction for GlimmerHMM_glimmerT_13838-T1
Valid prediction for snap_scaffold_5-snap.3650-T1
Valid prediction for snap_scaffold_5-snap.3629-T1
Valid prediction for snap_scaffold_5-snap.3644-T1
Valid prediction for Augustus_model.g9189.t1
Valid prediction for GlimmerHMM_glimmerT_13815-T1
Valid prediction for Augustus_model.g9192.t1
Valid prediction for HiQ_model.g9187.t1
Valid prediction for snap_scaffold_5-snap.3620-T1
Valid prediction for snap_scaffold_5-snap.3641-T1
Valid prediction for pasa_asmbl_44905.p1
Valid prediction for snap_scaffold_5-snap.3631-T1
Valid prediction for GlimmerHMM_glimmerT_13816-T1
Valid prediction for pasa_asmbl_44913.p1
Valid prediction for HiQ_model.g9198.t1
Valid prediction for GlimmerHMM_glimmerT_13842-T1
Valid prediction for GlimmerHMM_glimmerT_13812-T1
Valid prediction for Augustus_model.g9205.t1
Valid prediction for Augustus_model.g9183.t1
Valid prediction for GlimmerHMM_glimmerT_13841-T1
Valid prediction for GlimmerHMM_glimmerT_13837-T1
Valid prediction for GlimmerHMM_glimmerT_13826-T1
Valid prediction for snap_scaffold_5-snap.3624-T1
Valid prediction for GlimmerHMM_glimmerT_13814-T1
Valid prediction for snap_scaffold_5-snap.3618-T1
Valid prediction for Augustus_model.g9188.t1
Valid prediction for GlimmerHMM_glimmerT_13829-T1
Valid prediction for GlimmerHMM_glimmerT_13839-T1
Valid prediction for GlimmerHMM_glimmerT_13832-T1
Valid prediction for GlimmerHMM_glimmerT_13817-T1
Valid prediction for Augustus_model.g9199.t1
Valid prediction for Augustus_model.g9184.t1
Valid prediction for snap_scaffold_5-snap.3627-T1
Valid prediction for snap_scaffold_5-snap.3636-T1
Valid prediction for Augustus_model.g9190.t1
Valid prediction for GlimmerHMM_glimmerT_13821-T1
Valid prediction for snap_scaffold_5-snap.3643-T1
Valid prediction for snap_scaffold_5-snap.3626-T1
Valid prediction for Augustus_model.g9206.t1
Valid prediction for GlimmerHMM_glimmerT_13836-T1
Valid prediction for GlimmerHMM_glimmerT_13824-T1
Valid prediction for snap_scaffold_5-snap.3640-T1
Valid prediction for snap_scaffold_5-snap.3619-T1
Valid prediction for GlimmerHMM_glimmerT_13840-T1
Valid prediction for Augustus_model.g9191.t1
Valid prediction for GlimmerHMM_glimmerT_13834-T1
Valid prediction for snap_scaffold_5-snap.3628-T1

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

-building trellis in range 1 - 194581
-exon list size: 300


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    
6.0    
6.3    
6.6    
7.0    
7.3    
7.6    
7.9    
8.3    
8.6    
8.9    
9.3    
9.6    
9.9    
10.3    
10.6    
10.9    
11.3    
11.6    
11.9    
12.3    
12.6    
12.9    
13.2    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.9    
18.2    
18.5    
18.9    
19.2    
19.5    
19.9    
20.2    
20.5    
20.9    
21.2    
21.5    
21.9    
22.2    
22.5    
22.8    
23.2    
23.5    
23.8    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.2    
26.5    
26.8    
27.2    
27.5    
27.8    
28.1    
28.5    
28.8    
29.1    
29.5    
29.8    
30.1    
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    
35.8    
36.1    
36.4    
36.8    
37.1    
37.4    
37.7    
38.1    
38.4    
38.7    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.4    
43.7    
44.0    
44.4    
44.7    
45.0    
45.4    
45.7    
46.0    
46.4    
46.7    
47.0    
47.4    
47.7    
48.0    
48.3    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.7    
52.0    
52.3    
52.6    
53.0    
53.3    
53.6    
54.0    
54.3    
54.6    
55.0    
55.3    
55.6    
56.0    
56.3    
56.6    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.3    
61.6    
61.9    
62.3    
62.6    
62.9    
63.2    
63.6    
63.9    
64.2    
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    
69.9    
70.2    
70.5    
70.9    
71.2    
71.5    
71.9    
72.2    
72.5    
72.8    
73.2    
73.5    
73.8    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.2    
76.5    
76.8    
77.2    
77.5    
77.8    
78.1    
78.5    
78.8    
79.1    
79.5    
79.8    
80.1    
80.5    
80.8    
81.1    
81.5    
81.8    
82.1    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.8    
87.1    
87.4    
87.7    
88.1    
88.4    
88.7    
89.1    
89.4    
89.7    
90.1    
90.4    
90.7    
91.1    
91.4    
91.7    
92.1    
92.4    
92.7    
93.0    
93.4    
93.7    
94.0    
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 40 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support