-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_13746499-13918117

-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_7648-T1
Valid prediction for pasa_asmbl_40467.p1
Valid prediction for CodingQuarry_transcript_46335-T1
Valid prediction for GlimmerHMM_glimmerT_7659-T1
Valid prediction for snap_scaffold_3-snap.2649-T1
Valid prediction for snap_scaffold_3-snap.2642-T1
Valid prediction for snap_scaffold_3-snap.2647-T1
Valid prediction for HiQ_model.g5018.t1
Valid prediction for Augustus_model.g5015.t1
Valid prediction for snap_scaffold_3-snap.2660-T1
Valid prediction for snap_scaffold_3-snap.2655-T1
Valid prediction for snap_scaffold_3-snap.2646-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g5009.t1
Valid prediction for GlimmerHMM_glimmerT_7643-T1
Valid prediction for GlimmerHMM_glimmerT_7660-T1
Valid prediction for snap_scaffold_3-snap.2654-T1
Valid prediction for GlimmerHMM_glimmerT_7645-T1
Valid prediction for snap_scaffold_3-snap.2653-T1
Valid prediction for snap_scaffold_3-snap.2635-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2645-T1
Valid prediction for CodingQuarry_transcript_46336-T1
Valid prediction for snap_scaffold_3-snap.2641-T1
Valid prediction for snap_scaffold_3-snap.2656-T1
Valid prediction for snap_scaffold_3-snap.2651-T1
Valid prediction for GlimmerHMM_glimmerT_7655-T1
Valid prediction for GlimmerHMM_glimmerT_7663-T1
Valid prediction for GlimmerHMM_glimmerT_7661-T1
Valid prediction for snap_scaffold_3-snap.2659-T1
Couldn't classify 21670, 21823
Sorry, prediction pasa_asmbl_40458.p1 fails validation.
(AGT)	 TC	21670-21823	GT	AGG
(ATC)	 AG	22429-22556	GT	AGG
(GTC)	 AG	22656-22817	TA	AGT
-recovered pasa_asmbl_40458.p1, terminal, 22656, 22817
-recovered pasa_asmbl_40458.p1, internal, 22429, 22556
Valid prediction for GlimmerHMM_glimmerT_7638-T1
Valid prediction for snap_scaffold_3-snap.2639-T1
Valid prediction for HiQ_model.g5028.t1
Valid prediction for snap_scaffold_3-snap.2638-T1
Valid prediction for GlimmerHMM_glimmerT_7662-T1
Valid prediction for Augustus_model.g5022.t1
Valid prediction for Augustus_model.g5026.t1
Valid prediction for Augustus_model.g5024.t1
Valid prediction for pasa_asmbl_40461.p1
Valid prediction for Augustus_model.g5025.t1
Valid prediction for HiQ_model.g5027.t1
Valid prediction for snap_scaffold_3-snap.2643-T1
Valid prediction for snap_scaffold_3-snap.2658-T1
Valid prediction for Augustus_model.g5007.t1
Valid prediction for GlimmerHMM_glimmerT_7654-T1
Valid prediction for Augustus_model.g5005.t1
Couldn't classify 156444, 156776
Sorry, prediction pasa_asmbl_40470.p1 fails validation.
(TGC)	 GT	156444-156776	GT	TGG
(CAA)	 AG	157656-158036	AC	GAA
-recovered pasa_asmbl_40470.p1, terminal, 157656, 158036
Valid prediction for Augustus_model.g5011.t1
Valid prediction for snap_scaffold_3-snap.2648-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7640-T1
Valid prediction for GlimmerHMM_glimmerT_7657-T1
Valid prediction for snap_scaffold_3-snap.2657-T1
Valid prediction for snap_scaffold_3-snap.2644-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 Augustus_model.g5019.t1
Valid prediction for Augustus_model.g5012.t1
Valid prediction for snap_scaffold_3-snap.2640-T1
Valid prediction for snap_scaffold_3-snap.2636-T1
Valid prediction for GlimmerHMM_glimmerT_7642-T1
Valid prediction for GlimmerHMM_glimmerT_7647-T1
Valid prediction for pasa_asmbl_39299.p1
Valid prediction for snap_scaffold_3-snap.2650-T1
Valid prediction for HiQ_model.g5016.t1
Valid prediction for snap_scaffold_3-snap.2652-T1
Valid prediction for GlimmerHMM_glimmerT_7649-T1
Valid prediction for GlimmerHMM_glimmerT_7650-T1
Valid prediction for GlimmerHMM_glimmerT_7656-T1
Valid prediction for GlimmerHMM_glimmerT_7651-T1
Valid prediction for HiQ_model.g5021.t1
Valid prediction for GlimmerHMM_glimmerT_7646-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_46333-T1
Valid prediction for Augustus_model.g5020.t1
Valid prediction for GlimmerHMM_glimmerT_7641-T1
Valid prediction for Augustus_model.g5023.t1
Valid prediction for Augustus_model.g5006.t1
Valid prediction for GlimmerHMM_glimmerT_7644-T1
Valid prediction for Augustus_model.g5014.t1
Valid prediction for snap_scaffold_3-snap.2637-T1
Couldn't classify 116714, 116871
Couldn't classify 121433, 121516
Sorry, prediction pasa_asmbl_39302.p1 fails validation.
(TTT)	 GG	116714-116871	GT	AGG
(CTC)	 AG	117097-117189	GT	AGG
(ACT)	 AG	117949-118008	GT	AAG
(GGA)	 AG	118512-118532	GT	TTG
(AAA)	 AG	119306-119399	GT	TGG
(CAG)	 AG	119704-119748	GT	AGG
(GGT)	 AG	121433-121516	GT	AAG
add_exon() Sorry, pasa_asmbl_39302.p1 117949-118008-terminal-1 is invalid.
-recovered pasa_asmbl_39302.p1, terminal, 117949, 118008
-recovered pasa_asmbl_39302.p1, internal, 117097, 117189
-recovered pasa_asmbl_39302.p1, internal, 117949, 118008
-recovered pasa_asmbl_39302.p1, internal, 118512, 118532
-recovered pasa_asmbl_39302.p1, internal, 119306, 119399
-recovered pasa_asmbl_39302.p1, internal, 119704, 119748
-recovered pasa_asmbl_39302.p1, internal, 121433, 121516
Couldn't classify 91379, 91513
Couldn't classify 92701, 92793
Sorry, prediction pasa_asmbl_39684.p1 fails validation.
(GAC)	 GG	91379-91513	GT	AGG
(GGG)	 AG	92460-92558	GT	AGG
(GGT)	 AG	92701-92793	GT	AGG
-recovered pasa_asmbl_39684.p1, internal, 92460, 92558
-recovered pasa_asmbl_39684.p1, internal, 92701, 92793
Valid prediction for GlimmerHMM_glimmerT_7639-T1
Valid prediction for Augustus_model.g5013.t1
Valid prediction for Augustus_model.g5017.t1
Valid prediction for GlimmerHMM_glimmerT_7652-T1
Valid prediction for GlimmerHMM_glimmerT_7658-T1
Valid prediction for HiQ_model.g5010.t1
Valid prediction for GlimmerHMM_glimmerT_7653-T1
Valid prediction for Augustus_model.g5008.t1

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

-building trellis in range 1 - 171619
-exon list size: 263


building trellis

0.4    
0.8    
1.1    
1.5    
1.9    
2.3    
2.6    
3.0    
3.4    
3.8    
4.2    
4.5    
4.9    
5.3    
5.7    
6.0    
6.4    
6.8    
7.2    
7.5    
7.9    
8.3    
8.7    
9.1    
9.4    
9.8    
10.2    
10.6    
10.9    
11.3    
11.7    
12.1    
12.5    
12.8    
13.2    
13.6    
14.0    
14.3    
14.7    
15.1    
15.5    
15.8    
16.2    
16.6    
17.0    
17.4    
17.7    
18.1    
18.5    
18.9    
19.2    
19.6    
20.0    
20.4    
20.8    
21.1    
21.5    
21.9    
22.3    
22.6    
23.0    
23.4    
23.8    
24.2    
24.5    
24.9    
25.3    
25.7    
26.0    
26.4    
26.8    
27.2    
27.5    
27.9    
28.3    
28.7    
29.1    
29.4    
29.8    
30.2    
30.6    
30.9    
31.3    
31.7    
32.1    
32.5    
32.8    
33.2    
33.6    
34.0    
34.3    
34.7    
35.1    
35.5    
35.8    
36.2    
36.6    
37.0    
37.4    
37.7    
38.1    
38.5    
38.9    
39.2    
39.6    
40.0    
40.4    
40.8    
41.1    
41.5    
41.9    
42.3    
42.6    
43.0    
43.4    
43.8    
44.2    
44.5    
44.9    
45.3    
45.7    
46.0    
46.4    
46.8    
47.2    
47.5    
47.9    
48.3    
48.7    
49.1    
49.4    
49.8    
50.2    
50.6    
50.9    
51.3    
51.7    
52.1    
52.5    
52.8    
53.2    
53.6    
54.0    
54.3    
54.7    
55.1    
55.5    
55.8    
56.2    
56.6    
57.0    
57.4    
57.7    
58.1    
58.5    
58.9    
59.2    
59.6    
60.0    
60.4    
60.8    
61.1    
61.5    
61.9    
62.3    
62.6    
63.0    
63.4    
63.8    
64.2    
64.5    
64.9    
65.3    
65.7    
66.0    
66.4    
66.8    
67.2    
67.5    
67.9    
68.3    
68.7    
69.1    
69.4    
69.8    
70.2    
70.6    
70.9    
71.3    
71.7    
72.1    
72.5    
72.8    
73.2    
73.6    
74.0    
74.3    
74.7    
75.1    
75.5    
75.8    
76.2    
76.6    
77.0    
77.4    
77.7    
78.1    
78.5    
78.9    
79.2    
79.6    
80.0    
80.4    
80.8    
81.1    
81.5    
81.9    
82.3    
82.6    
83.0    
83.4    
83.8    
84.2    
84.5    
84.9    
85.3    
85.7    
86.0    
86.4    
86.8    
87.2    
87.5    
87.9    
88.3    
88.7    
89.1    
89.4    
89.8    
90.2    
90.6    
90.9    
91.3    
91.7    
92.1    
92.5    
92.8    
93.2    
93.6    
94.0    
94.3    
94.7    
95.1    
95.5    
95.8    
96.2    
96.6    
97.0    
97.4    
97.7    
98.1    
98.5    
98.9    
99.2    
99.6    
-found 29 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 158037 - 171619
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 158037 - 169512
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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