-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_12980639-13155537

-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_7685-T1
Valid prediction for GeneMark_model.12702_t
Valid prediction for GeneMark_model.12709_t
Valid prediction for GeneMark_model.12699_t
Valid prediction for snap_scaffold_3-snap.2546-T1
Valid prediction for GeneMark_model.12695_t
Valid prediction for GlimmerHMM_glimmerT_7708-T1
Valid prediction for Augustus_model.g5065.t1
Valid prediction for GlimmerHMM_glimmerT_7711-T1
Valid prediction for Augustus_model.g5071.t1
Valid prediction for GeneMark_model.12706_t
Valid prediction for GlimmerHMM_glimmerT_7702-T1
Valid prediction for GeneMark_model.12694_t
Valid prediction for GlimmerHMM_glimmerT_7715-T1
Valid prediction for GlimmerHMM_glimmerT_7700-T1
Valid prediction for snap_scaffold_3-snap.2531-T1
Valid prediction for Augustus_model.g5068.t1
Valid prediction for snap_scaffold_3-snap.2543-T1
Valid prediction for GlimmerHMM_glimmerT_7697-T1
Valid prediction for GlimmerHMM_glimmerT_7713-T1
Valid prediction for GeneMark_model.12691_t
Valid prediction for snap_scaffold_3-snap.2547-T1
Valid prediction for GlimmerHMM_glimmerT_7716-T1
Valid prediction for GeneMark_model.12708_t
Valid prediction for GeneMark_model.12690_t
Valid prediction for snap_scaffold_3-snap.2526-T1
Valid prediction for snap_scaffold_3-snap.2544-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g5062.t1
Valid prediction for GlimmerHMM_glimmerT_7692-T1
Valid prediction for GlimmerHMM_glimmerT_7703-T1
Valid prediction for GeneMark_model.12713_t
Valid prediction for snap_scaffold_3-snap.2538-T1
Valid prediction for snap_scaffold_3-snap.2549-T1
Valid prediction for GeneMark_model.12689_t
Valid prediction for Augustus_model.g5055.t1
Valid prediction for GeneMark_model.12703_t
Valid prediction for Augustus_model.g5060.t1
Valid prediction for Augustus_model.g5056.t1
Valid prediction for HiQ_model.g5070.t1
Valid prediction for CodingQuarry_transcript_46207-T1
Valid prediction for GlimmerHMM_glimmerT_7688-T1
Valid prediction for pasa_asmbl_40376.p1
Valid prediction for snap_scaffold_3-snap.2527-T1
Valid prediction for Augustus_model.g5050.t1
Valid prediction for GlimmerHMM_glimmerT_7686-T1
Valid prediction for Augustus_model.g5066.t1
Valid prediction for GlimmerHMM_glimmerT_7691-T1
Valid prediction for GlimmerHMM_glimmerT_7704-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.12711_t
Valid prediction for Augustus_model.g5052.t1
Valid prediction for snap_scaffold_3-snap.2536-T1
Valid prediction for GeneMark_model.12716_t
Valid prediction for snap_scaffold_3-snap.2532-T1
Valid prediction for snap_scaffold_3-snap.2530-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: -)Couldn't classify 61130, 62260
Sorry, prediction pasa_asmbl_40374.p1 fails validation.
(TCG)	 CA	61130-62260	AG	CTA
Valid prediction for snap_scaffold_3-snap.2534-T1
Valid prediction for GlimmerHMM_glimmerT_7687-T1
Valid prediction for GlimmerHMM_glimmerT_7699-T1
Valid prediction for snap_scaffold_3-snap.2537-T1
Valid prediction for snap_scaffold_3-snap.2533-T1
Valid prediction for Augustus_model.g5058.t1
Valid prediction for snap_scaffold_3-snap.2542-T1
Valid prediction for snap_scaffold_3-snap.2548-T1
Valid prediction for GeneMark_model.12700_t
Valid prediction for GlimmerHMM_glimmerT_7705-T1
Valid prediction for GeneMark_model.12710_t
Valid prediction for GeneMark_model.12693_t
Valid prediction for GlimmerHMM_glimmerT_7706-T1
Valid prediction for GlimmerHMM_glimmerT_7698-T1
Valid prediction for GeneMark_model.12698_t
Valid prediction for GlimmerHMM_glimmerT_7695-T1
Valid prediction for GlimmerHMM_glimmerT_7690-T1
Valid prediction for snap_scaffold_3-snap.2535-T1
Valid prediction for Augustus_model.g5051.t1
Valid prediction for snap_scaffold_3-snap.2541-T1
Valid prediction for GlimmerHMM_glimmerT_7707-T1
Valid prediction for snap_scaffold_3-snap.2529-T1
Valid prediction for Augustus_model.g5069.t1
Valid prediction for Augustus_model.g5059.t1
Valid prediction for Augustus_model.g5067.t1
Valid prediction for GlimmerHMM_glimmerT_7714-T1
Valid prediction for GeneMark_model.12697_t
Valid prediction for snap_scaffold_3-snap.2545-T1
Valid prediction for Augustus_model.g5064.t1
Valid prediction for Augustus_model.g5053.t1
Valid prediction for GlimmerHMM_glimmerT_7693-T1
Valid prediction for GeneMark_model.12692_t
Valid prediction for GlimmerHMM_glimmerT_7701-T1
Valid prediction for snap_scaffold_3-snap.2539-T1
Valid prediction for GeneMark_model.12715_t
Valid prediction for GlimmerHMM_glimmerT_7712-T1
Valid prediction for GlimmerHMM_glimmerT_7689-T1
Valid prediction for Augustus_model.g5057.t1
Valid prediction for GlimmerHMM_glimmerT_7696-T1
Valid prediction for Augustus_model.g5061.t1
Valid prediction for GeneMark_model.12704_t
Valid prediction for GlimmerHMM_glimmerT_7694-T1
Valid prediction for GeneMark_model.12705_t
Valid prediction for GeneMark_model.12696_t
Valid prediction for GlimmerHMM_glimmerT_7709-T1
Valid prediction for Augustus_model.g5063.t1
Valid prediction for GlimmerHMM_glimmerT_7710-T1
Valid prediction for snap_scaffold_3-snap.2540-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g5054.t1
Valid prediction for snap_scaffold_3-snap.2528-T1

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

-building trellis in range 1 - 174899
-exon list size: 252


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.1    
3.5    
3.9    
4.3    
4.7    
5.1    
5.5    
5.9    
6.3    
6.7    
7.1    
7.5    
7.9    
8.3    
8.7    
9.1    
9.4    
9.8    
10.2    
10.6    
11.0    
11.4    
11.8    
12.2    
12.6    
13.0    
13.4    
13.8    
14.2    
14.6    
15.0    
15.4    
15.7    
16.1    
16.5    
16.9    
17.3    
17.7    
18.1    
18.5    
18.9    
19.3    
19.7    
20.1    
20.5    
20.9    
21.3    
21.7    
22.0    
22.4    
22.8    
23.2    
23.6    
24.0    
24.4    
24.8    
25.2    
25.6    
26.0    
26.4    
26.8    
27.2    
27.6    
28.0    
28.3    
28.7    
29.1    
29.5    
29.9    
30.3    
30.7    
31.1    
31.5    
31.9    
32.3    
32.7    
33.1    
33.5    
33.9    
34.3    
34.6    
35.0    
35.4    
35.8    
36.2    
36.6    
37.0    
37.4    
37.8    
38.2    
38.6    
39.0    
39.4    
39.8    
40.2    
40.6    
40.9    
41.3    
41.7    
42.1    
42.5    
42.9    
43.3    
43.7    
44.1    
44.5    
44.9    
45.3    
45.7    
46.1    
46.5    
46.9    
47.2    
47.6    
48.0    
48.4    
48.8    
49.2    
49.6    
50.0    
50.4    
50.8    
51.2    
51.6    
52.0    
52.4    
52.8    
53.1    
53.5    
53.9    
54.3    
54.7    
55.1    
55.5    
55.9    
56.3    
56.7    
57.1    
57.5    
57.9    
58.3    
58.7    
59.1    
59.4    
59.8    
60.2    
60.6    
61.0    
61.4    
61.8    
62.2    
62.6    
63.0    
63.4    
63.8    
64.2    
64.6    
65.0    
65.4    
65.7    
66.1    
66.5    
66.9    
67.3    
67.7    
68.1    
68.5    
68.9    
69.3    
69.7    
70.1    
70.5    
70.9    
71.3    
71.7    
72.0    
72.4    
72.8    
73.2    
73.6    
74.0    
74.4    
74.8    
75.2    
75.6    
76.0    
76.4    
76.8    
77.2    
77.6    
78.0    
78.3    
78.7    
79.1    
79.5    
79.9    
80.3    
80.7    
81.1    
81.5    
81.9    
82.3    
82.7    
83.1    
83.5    
83.9    
84.3    
84.6    
85.0    
85.4    
85.8    
86.2    
86.6    
87.0    
87.4    
87.8    
88.2    
88.6    
89.0    
89.4    
89.8    
90.2    
90.6    
90.9    
91.3    
91.7    
92.1    
92.5    
92.9    
93.3    
93.7    
94.1    
94.5    
94.9    
95.3    
95.7    
96.1    
96.5    
96.9    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 30 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10958
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support