-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_1131801-1359316

-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 pasa_asmbl_31320.p1
Valid prediction for snap_scaffold_23-snap.193-T1
Valid prediction for snap_scaffold_23-snap.164-T1
Valid prediction for GlimmerHMM_glimmerT_50459-T1
Valid prediction for snap_scaffold_23-snap.166-T1
Valid prediction for snap_scaffold_23-snap.177-T1
Valid prediction for snap_scaffold_23-snap.195-T1
Valid prediction for Augustus_model.g33687.t1
Valid prediction for Augustus_model.g33699.t1
Valid prediction for HiQ_model.g33706.t1
Valid prediction for Augustus_model.g33677.t1
Valid prediction for snap_scaffold_23-snap.197-T1
Valid prediction for snap_scaffold_23-snap.200-T1
Valid prediction for Augustus_model.g33679.t1
Valid prediction for GlimmerHMM_glimmerT_50460-T1
Valid prediction for snap_scaffold_23-snap.169-T1
Valid prediction for GlimmerHMM_glimmerT_50440-T1
Valid prediction for GlimmerHMM_glimmerT_50445-T1
Valid prediction for snap_scaffold_23-snap.190-T1
Valid prediction for GlimmerHMM_glimmerT_50450-T1
Valid prediction for GlimmerHMM_glimmerT_50474-T1
Valid prediction for snap_scaffold_23-snap.194-T1
Valid prediction for Augustus_model.g33690.t1
Valid prediction for snap_scaffold_23-snap.178-T1
Couldn't classify 56090, 56236
Couldn't classify 68292, 68383
Sorry, prediction pasa_asmbl_31314.p1 fails validation.
(GAG)	 CA	56090-56236	GT	AGG
(GTT)	 AG	56414-56476	GT	AGG
(ACT)	 AG	57040-57138	GT	TGG
(TCT)	 AG	57351-57444	GT	TGG
(ATG)	 AG	57642-57758	GT	TGG
(AGC)	 AG	57880-58031	GT	AGG
(GGG)	 AG	58233-58408	GT	TGG
(GGC)	 AG	58936-59092	GT	CGG
(TGC)	 AG	59712-59934	GT	TGG
(ATA)	 AG	61725-61840	GT	GGG
(ACT)	 AG	62453-62625	GT	CGG
(GAA)	 AG	62805-62851	GT	AGG
(CTC)	 AG	63391-63747	GT	AGG
(CTA)	 AG	65673-65903	GT	GGG
(GTC)	 AG	67210-67425	GT	AGG
(ATG)	 AG	68292-68383	GT	GGG
add_exon() Sorry, pasa_asmbl_31314.p1 57642-57758-initial-1 is invalid.
-recovered pasa_asmbl_31314.p1, initial, 57642, 57758
add_exon() Sorry, pasa_asmbl_31314.p1 68292-68383-initial-1 is invalid.
-recovered pasa_asmbl_31314.p1, initial, 68292, 68383
-recovered pasa_asmbl_31314.p1, internal, 56414, 56476
-recovered pasa_asmbl_31314.p1, internal, 57040, 57138
-recovered pasa_asmbl_31314.p1, internal, 57351, 57444
-recovered pasa_asmbl_31314.p1, internal, 57642, 57758
-recovered pasa_asmbl_31314.p1, internal, 57880, 58031
-recovered pasa_asmbl_31314.p1, internal, 58233, 58408
-recovered pasa_asmbl_31314.p1, internal, 58936, 59092
-recovered pasa_asmbl_31314.p1, internal, 59712, 59934
-recovered pasa_asmbl_31314.p1, internal, 61725, 61840
-recovered pasa_asmbl_31314.p1, internal, 62453, 62625
-recovered pasa_asmbl_31314.p1, internal, 62805, 62851
-recovered pasa_asmbl_31314.p1, internal, 63391, 63747
-recovered pasa_asmbl_31314.p1, internal, 65673, 65903
-recovered pasa_asmbl_31314.p1, internal, 67210, 67425
-recovered pasa_asmbl_31314.p1, internal, 68292, 68383
Valid prediction for HiQ_model.g33709.t1
Valid prediction for GlimmerHMM_glimmerT_50444-T1
Valid prediction for snap_scaffold_23-snap.161-T1
Valid prediction for snap_scaffold_23-snap.167-T1
Valid prediction for snap_scaffold_23-snap.183-T1
Valid prediction for snap_scaffold_23-snap.191-T1
Valid prediction for snap_scaffold_23-snap.163-T1
Valid prediction for Augustus_model.g33682.t1
Valid prediction for snap_scaffold_23-snap.158-T1
Valid prediction for snap_scaffold_23-snap.171-T1
Valid prediction for Augustus_model.g33697.t1
Valid prediction for Augustus_model.g33700.t1
Valid prediction for snap_scaffold_23-snap.168-T1
Valid prediction for GlimmerHMM_glimmerT_50467-T1
Valid prediction for Augustus_model.g33681.t1
Valid prediction for GlimmerHMM_glimmerT_50462-T1
Valid prediction for GlimmerHMM_glimmerT_50470-T1
Valid prediction for GlimmerHMM_glimmerT_50471-T1
Valid prediction for snap_scaffold_23-snap.165-T1
Valid prediction for GlimmerHMM_glimmerT_50463-T1
Valid prediction for Augustus_model.g33698.t1
Valid prediction for snap_scaffold_23-snap.170-T1
Valid prediction for snap_scaffold_23-snap.199-T1
Valid prediction for snap_scaffold_23-snap.172-T1
Valid prediction for snap_scaffold_23-snap.162-T1
Valid prediction for Augustus_model.g33694.t1
Valid prediction for snap_scaffold_23-snap.182-T1
Valid prediction for GlimmerHMM_glimmerT_50453-T1
Valid prediction for GlimmerHMM_glimmerT_50442-T1
Valid prediction for CodingQuarry_transcript_35547-T1
Valid prediction for GlimmerHMM_glimmerT_50455-T1
Valid prediction for GlimmerHMM_glimmerT_50468-T1
Valid prediction for Augustus_model.g33684.t1
Valid prediction for Augustus_model.g33702.t1
Valid prediction for snap_scaffold_23-snap.185-T1
Valid prediction for Augustus_model.g33707.t1
Valid prediction for GlimmerHMM_glimmerT_50441-T1
Valid prediction for Augustus_model.g33703.t1
Valid prediction for Augustus_model.g33711.t1
Valid prediction for snap_scaffold_23-snap.196-T1
Valid prediction for snap_scaffold_23-snap.187-T1
Valid prediction for Augustus_model.g33705.t1
Valid prediction for HiQ_model.g33683.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_50449-T1
Valid prediction for GlimmerHMM_glimmerT_50461-T1
Valid prediction for snap_scaffold_23-snap.189-T1
Valid prediction for GlimmerHMM_glimmerT_50446-T1
Valid prediction for GlimmerHMM_glimmerT_50457-T1
Valid prediction for Augustus_model.g33708.t1
Valid prediction for GlimmerHMM_glimmerT_50454-T1
Valid prediction for Augustus_model.g33691.t1
Valid prediction for snap_scaffold_23-snap.174-T1
Valid prediction for Augustus_model.g33692.t1
Valid prediction for snap_scaffold_23-snap.186-T1
Valid prediction for GlimmerHMM_glimmerT_50458-T1
Valid prediction for snap_scaffold_23-snap.188-T1
Valid prediction for GlimmerHMM_glimmerT_50466-T1
Valid prediction for GlimmerHMM_glimmerT_50448-T1
Valid prediction for snap_scaffold_23-snap.179-T1
Valid prediction for Augustus_model.g33680.t1
Couldn't classify 222783, 222929
Sorry, prediction pasa_asmbl_30627.p1 fails validation.
(ATG)	 TC	213517-213614	GT	AGG
(GCC)	 AG	214462-214591	GT	TGG
(AGT)	 AG	215220-215341	GT	ATG
(TTT)	 AG	217713-217776	GT	AGG
(GCA)	 AG	217882-217975	GT	ACG
(CGT)	 AG	218489-218659	GT	CAG
(ACT)	 AG	218754-218813	GT	AGG
(TGA)	 AG	219009-219212	GT	AGG
(GAA)	 AG	219955-220062	GT	AGG
(AAT)	 AG	220239-220345	GT	ACG
(GTG)	 AG	222318-222431	GT	CGG
(AAC)	 AG	222783-222929	AG	CTA
-recovered pasa_asmbl_30627.p1, initial, 213517, 213614
add_exon() Sorry, pasa_asmbl_30627.p1 219009-219212-terminal-1 is invalid.
-recovered pasa_asmbl_30627.p1, terminal, 219009, 219212
-recovered pasa_asmbl_30627.p1, internal, 214462, 214591
-recovered pasa_asmbl_30627.p1, internal, 215220, 215341
-recovered pasa_asmbl_30627.p1, internal, 217713, 217776
-recovered pasa_asmbl_30627.p1, internal, 217882, 217975
-recovered pasa_asmbl_30627.p1, internal, 218489, 218659
-recovered pasa_asmbl_30627.p1, internal, 218754, 218813
-recovered pasa_asmbl_30627.p1, internal, 219009, 219212
-recovered pasa_asmbl_30627.p1, internal, 219955, 220062
-recovered pasa_asmbl_30627.p1, internal, 220239, 220345
-recovered pasa_asmbl_30627.p1, internal, 222318, 222431
Valid prediction for GlimmerHMM_glimmerT_50452-T1
Valid prediction for GlimmerHMM_glimmerT_50456-T1
Valid prediction for Augustus_model.g33704.t1
Valid prediction for snap_scaffold_23-snap.159-T1
Valid prediction for snap_scaffold_23-snap.198-T1
Valid prediction for GlimmerHMM_glimmerT_50447-T1
Valid prediction for Augustus_model.g33695.t1
Valid prediction for GlimmerHMM_glimmerT_50465-T1
Valid prediction for CodingQuarry_transcript_35546-T1
Valid prediction for Augustus_model.g33688.t1
Valid prediction for GlimmerHMM_glimmerT_50472-T1
Valid prediction for snap_scaffold_23-snap.180-T1
Valid prediction for Augustus_model.g33701.t1
Valid prediction for snap_scaffold_23-snap.181-T1
Valid prediction for Augustus_model.g33685.t1
Valid prediction for GlimmerHMM_glimmerT_50464-T1
Valid prediction for GlimmerHMM_glimmerT_50451-T1
Valid prediction for snap_scaffold_23-snap.192-T1
Valid prediction for snap_scaffold_23-snap.160-T1
Valid prediction for HiQ_model.g33678.t1
Valid prediction for GlimmerHMM_glimmerT_50473-T1
Valid prediction for snap_scaffold_23-snap.184-T1
Valid prediction for Augustus_model.g33696.t1
Valid prediction for GlimmerHMM_glimmerT_50469-T1
Valid prediction for snap_scaffold_23-snap.173-T1
Valid prediction for Augustus_model.g33693.t1
Valid prediction for snap_scaffold_23-snap.175-T1
Valid prediction for GlimmerHMM_glimmerT_50439-T1
Valid prediction for GlimmerHMM_glimmerT_50443-T1
Valid prediction for snap_scaffold_23-snap.176-T1
Valid prediction for Augustus_model.g33710.t1
Valid prediction for HiQ_model.g33689.t1
Valid prediction for Augustus_model.g33686.t1

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

-building trellis in range 1 - 227516
-exon list size: 325


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 45 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support