-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_29

-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 GlimmerHMM_glimmerT_59443-T1
Valid prediction for snap_scaffold_29-snap.10-T1
Valid prediction for snap_scaffold_29-snap.8-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_29-snap.3-T1
Valid prediction for Augustus_model.g39380.t1
Valid prediction for GlimmerHMM_glimmerT_59444-T1
Valid prediction for Augustus_model.g39384.t1
Valid prediction for snap_scaffold_29-snap.11-T1
Valid prediction for snap_scaffold_29-snap.6-T1
Valid prediction for GlimmerHMM_glimmerT_59435-T1
Valid prediction for GlimmerHMM_glimmerT_59441-T1
Valid prediction for GlimmerHMM_glimmerT_59436-T1
Valid prediction for snap_scaffold_29-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_59448-T1
Valid prediction for snap_scaffold_29-snap.2-T1
Valid prediction for Augustus_model.g39375.t1
Valid prediction for GlimmerHMM_glimmerT_59446-T1
Valid prediction for snap_scaffold_29-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_59437-T1
Valid prediction for snap_scaffold_29-snap.7-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 GlimmerHMM_glimmerT_59442-T1
Valid prediction for snap_scaffold_29-snap.15-T1
Valid prediction for GlimmerHMM_glimmerT_59452-T1
Valid prediction for Augustus_model.g39376.t1
Couldn't classify 396, 1065
Sorry, prediction snap_scaffold_29-snap.16-T1 fails validation.
(TCC)	 AG	396-1065	GT	TGG
(CCC)	 AG	1244-1520	GT	TGG
(ATT)	 AG	2507-2898	TC	GAT
-recovered snap_scaffold_29-snap.16-T1, terminal, 2507, 2898
-recovered snap_scaffold_29-snap.16-T1, internal, 396, 1065
-recovered snap_scaffold_29-snap.16-T1, internal, 1244, 1520
Valid prediction for snap_scaffold_29-snap.13-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_29-snap.5-T1
Valid prediction for Augustus_model.g39378.t1
Valid prediction for GlimmerHMM_glimmerT_59453-T1
add_exon() Sorry, GlimmerHMM_glimmerT_59453-T1 2532-2898-terminal-1 is invalid.
Couldn't classify 184, 648
Sorry, prediction pasa_asmbl_38635.p1 fails validation.
(CCA)	 AC	184-648	CC	CAC
Valid prediction for Augustus_model.g39379.t1
Valid prediction for GlimmerHMM_glimmerT_59439-T1
Valid prediction for GlimmerHMM_glimmerT_59440-T1
Valid prediction for Augustus_model.g39381.t1
Valid prediction for snap_scaffold_29-snap.12-T1
Valid prediction for Augustus_model.g39382.t1
Valid prediction for GlimmerHMM_glimmerT_59450-T1
Valid prediction for snap_scaffold_29-snap.4-T1
Valid prediction for snap_scaffold_29-snap.14-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_59445-T1
Valid prediction for Augustus_model.g39383.t1
Valid prediction for GlimmerHMM_glimmerT_59451-T1
Valid prediction for GlimmerHMM_glimmerT_59447-T1
Valid prediction for GlimmerHMM_glimmerT_59449-T1
Couldn't classify 47201, 47421
Sorry, prediction pasa_asmbl_38630.p1 fails validation.
(AAT)	 CC	47201-47421	GT	AGG
(GTC)	 AG	49179-49284	TG	GAT
-recovered pasa_asmbl_38630.p1, terminal, 49179, 49284
Valid prediction for Augustus_model.g39377.t1
Couldn't classify 715, 1188
Sorry, prediction pasa_asmbl_38634.p1 fails validation.
(TCC)	 CT	715-1188	AA	ATA
Valid prediction for GlimmerHMM_glimmerT_59438-T1

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

-building trellis in range 1 - 58417
-exon list size: 153


building trellis

0.6    
1.3    
1.9    
2.6    
3.2    
3.9    
4.5    
5.2    
5.8    
6.5    
7.1    
7.7    
8.4    
9.0    
9.7    
10.3    
11.0    
11.6    
12.3    
12.9    
13.5    
14.2    
14.8    
15.5    
16.1    
16.8    
17.4    
18.1    
18.7    
19.4    
20.0    
20.6    
21.3    
21.9    
22.6    
23.2    
23.9    
24.5    
25.2    
25.8    
26.5    
27.1    
27.7    
28.4    
29.0    
29.7    
30.3    
31.0    
31.6    
32.3    
32.9    
33.5    
34.2    
34.8    
35.5    
36.1    
36.8    
37.4    
38.1    
38.7    
39.4    
40.0    
40.6    
41.3    
41.9    
42.6    
43.2    
43.9    
44.5    
45.2    
45.8    
46.5    
47.1    
47.7    
48.4    
49.0    
49.7    
50.3    
51.0    
51.6    
52.3    
52.9    
53.5    
54.2    
54.8    
55.5    
56.1    
56.8    
57.4    
58.1    
58.7    
59.4    
60.0    
60.6    
61.3    
61.9    
62.6    
63.2    
63.9    
64.5    
65.2    
65.8    
66.5    
67.1    
67.7    
68.4    
69.0    
69.7    
70.3    
71.0    
71.6    
72.3    
72.9    
73.5    
74.2    
74.8    
75.5    
76.1    
76.8    
77.4    
78.1    
78.7    
79.4    
80.0    
80.6    
81.3    
81.9    
82.6    
83.2    
83.9    
84.5    
85.2    
85.8    
86.5    
87.1    
87.7    
88.4    
89.0    
89.7    
90.3    
91.0    
91.6    
92.3    
92.9    
93.5    
94.2    
94.8    
95.5    
96.1    
96.8    
97.4    
98.1    
98.7    
99.4    
-found 23 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support