-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_4606471-4812184

-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 GeneMark_model.677_t
Valid prediction for GeneMark_model.687_t
Valid prediction for GeneMark_model.671_t
Valid prediction for GlimmerHMM_glimmerT_561-T1
Valid prediction for snap_scaffold_1-snap.712-T1
Valid prediction for GeneMark_model.660_t
Valid prediction for snap_scaffold_1-snap.718-T1
Valid prediction for snap_scaffold_1-snap.716-T1
Couldn't classify 3895, 4019
Couldn't classify 4629, 5700
Sorry, prediction pasa_asmbl_1680.p1 fails validation.
(GAG)	 CC	3895-4019	GT	AGG
(GTT)	 AG	4629-5700	GG	ATG
Valid prediction for snap_scaffold_1-snap.698-T1
Valid prediction for GlimmerHMM_glimmerT_556-T1
Valid prediction for GlimmerHMM_glimmerT_565-T1
Valid prediction for snap_scaffold_1-snap.697-T1
Valid prediction for GeneMark_model.691_t
Valid prediction for snap_scaffold_1-snap.710-T1
Valid prediction for Augustus_model.g437.t1
Valid prediction for CodingQuarry_transcript_2592-T1
Valid prediction for snap_scaffold_1-snap.704-T1
Valid prediction for GlimmerHMM_glimmerT_571-T1
Valid prediction for GeneMark_model.690_t
Valid prediction for snap_scaffold_1-snap.717-T1
Valid prediction for snap_scaffold_1-snap.709-T1
Valid prediction for GlimmerHMM_glimmerT_562-T1
Valid prediction for snap_scaffold_1-snap.719-T1
Valid prediction for GeneMark_model.658_t
Valid prediction for snap_scaffold_1-snap.708-T1
Valid prediction for GeneMark_model.669_t
Valid prediction for snap_scaffold_1-snap.707-T1
Valid prediction for snap_scaffold_1-snap.713-T1
Valid prediction for Augustus_model.g436.t1
Valid prediction for GlimmerHMM_glimmerT_566-T1
Valid prediction for Augustus_model.g431.t1
Valid prediction for snap_scaffold_1-snap.714-T1
Valid prediction for GeneMark_model.665_t
Valid prediction for GlimmerHMM_glimmerT_572-T1
Valid prediction for snap_scaffold_1-snap.720-T1
Valid prediction for GeneMark_model.662_t
Valid prediction for GeneMark_model.680_t
Valid prediction for Augustus_model.g430.t1
Valid prediction for snap_scaffold_1-snap.711-T1
Valid prediction for GeneMark_model.675_t
Valid prediction for GeneMark_model.673_t
Valid prediction for Augustus_model.g435.t1
Valid prediction for GlimmerHMM_glimmerT_568-T1
Valid prediction for GeneMark_model.682_t
Valid prediction for GlimmerHMM_glimmerT_552-T1
Valid prediction for Augustus_model.g432.t1
Valid prediction for Augustus_model.g434.t1
Valid prediction for GlimmerHMM_glimmerT_560-T1
Valid prediction for GeneMark_model.679_t
Valid prediction for GeneMark_model.667_t
Valid prediction for snap_scaffold_1-snap.715-T1
Valid prediction for snap_scaffold_1-snap.702-T1
Valid prediction for GeneMark_model.664_t
Valid prediction for GlimmerHMM_glimmerT_564-T1
Valid prediction for snap_scaffold_1-snap.706-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_553-T1
Valid prediction for GeneMark_model.685_t
Valid prediction for GeneMark_model.683_t
Couldn't classify 6233, 6412
Sorry, prediction pasa_asmbl_1682.p1 fails validation.
(TTT)	 AG	6233-6412	GT	AGG
(ACA)	 AG	6637-6743	GT	AGG
(GTA)	 AG	7040-7278	GT	AGG
(GAA)	 AG	7404-7535	GT	GGG
(GGA)	 AG	7729-7877	GT	AGG
(ATC)	 AG	8025-8168	GT	CGG
(GGG)	 AG	8482-8596	GT	AGG
(ACA)	 AG	8814-9046	GT	AGG
(ATT)	 AG	9352-9491	GT	CGG
(GTT)	 AG	9880-10180	GT	AGG
(CTC)	 AG	11925-12035	GT	AGG
(CAC)	 AG	12198-12293	GT	AGG
(GGC)	 AG	12443-14884	AT	AAA
-recovered pasa_asmbl_1682.p1, terminal, 12443, 14884
-recovered pasa_asmbl_1682.p1, internal, 6233, 6412
-recovered pasa_asmbl_1682.p1, internal, 6637, 6743
-recovered pasa_asmbl_1682.p1, internal, 7040, 7278
-recovered pasa_asmbl_1682.p1, internal, 7404, 7535
-recovered pasa_asmbl_1682.p1, internal, 7729, 7877
-recovered pasa_asmbl_1682.p1, internal, 8025, 8168
-recovered pasa_asmbl_1682.p1, internal, 8482, 8596
-recovered pasa_asmbl_1682.p1, internal, 8814, 9046
-recovered pasa_asmbl_1682.p1, internal, 9352, 9491
-recovered pasa_asmbl_1682.p1, internal, 9880, 10180
-recovered pasa_asmbl_1682.p1, internal, 11925, 12035
-recovered pasa_asmbl_1682.p1, internal, 12198, 12293
Valid prediction for GeneMark_model.659_t
Valid prediction for Augustus_model.g433.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 GeneMark_model.666_t
Valid prediction for GlimmerHMM_glimmerT_569-T1
Valid prediction for GeneMark_model.668_t
Valid prediction for GlimmerHMM_glimmerT_557-T1
Valid prediction for GeneMark_model.692_t
Valid prediction for GeneMark_model.688_t
Valid prediction for GeneMark_model.678_t
Valid prediction for GlimmerHMM_glimmerT_555-T1
Valid prediction for GeneMark_model.689_t
Valid prediction for GeneMark_model.674_t
Valid prediction for GlimmerHMM_glimmerT_570-T1
Valid prediction for GeneMark_model.684_t
Valid prediction for Augustus_model.g429.t1
Valid prediction for GlimmerHMM_glimmerT_559-T1
Valid prediction for snap_scaffold_1-snap.703-T1
Valid prediction for GeneMark_model.672_t
Valid prediction for GlimmerHMM_glimmerT_558-T1
Valid prediction for GeneMark_model.661_t
Valid prediction for GlimmerHMM_glimmerT_563-T1
Valid prediction for snap_scaffold_1-snap.705-T1
Valid prediction for GeneMark_model.663_t
Valid prediction for GlimmerHMM_glimmerT_554-T1
Valid prediction for GeneMark_model.670_t
Valid prediction for snap_scaffold_1-snap.700-T1
Valid prediction for GeneMark_model.676_t
Valid prediction for snap_scaffold_1-snap.701-T1
Valid prediction for snap_scaffold_1-snap.699-T1
Valid prediction for GlimmerHMM_glimmerT_567-T1
Valid prediction for GeneMark_model.681_t

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

-building trellis in range 1 - 205714
-exon list size: 352


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.9    
23.2    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.8    
27.1    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.9    
73.2    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.8    
77.1    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 24 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support