-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_18420302-18638009

-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_21402-T1
Valid prediction for snap_scaffold_8-snap.3421-T1
Valid prediction for GlimmerHMM_glimmerT_21416-T1
Valid prediction for pasa_asmbl_53544.p1
Valid prediction for snap_scaffold_8-snap.3422-T1
Valid prediction for snap_scaffold_8-snap.3413-T1
Valid prediction for snap_scaffold_8-snap.3404-T1
Valid prediction for snap_scaffold_8-snap.3407-T1
Valid prediction for GlimmerHMM_glimmerT_21400-T1
Valid prediction for CodingQuarry_transcript_59964-T1
Valid prediction for GlimmerHMM_glimmerT_21395-T1
Valid prediction for HiQ_model.g14260.t1
Valid prediction for CodingQuarry_transcript_59967-T1
Valid prediction for snap_scaffold_8-snap.3392-T1
Valid prediction for GlimmerHMM_glimmerT_21412-T1
Valid prediction for snap_scaffold_8-snap.3393-T1
Valid prediction for pasa_asmbl_53558.p1
Valid prediction for HiQ_model.g14258.t1
Valid prediction for pasa_asmbl_53567.p1
Valid prediction for GlimmerHMM_glimmerT_21405-T1
Valid prediction for Augustus_model.g14267.t1
Valid prediction for CodingQuarry_transcript_59968-T1
Valid prediction for GlimmerHMM_glimmerT_21393-T1
Valid prediction for snap_scaffold_8-snap.3406-T1
Couldn't classify 4907, 4948
Sorry, prediction pasa_asmbl_53548.p2 fails validation.
(ATG)	 TT	3683-3722	GT	ACG
(AGG)	 AG	3885-4015	GT	TGG
(AGT)	 AG	4271-4388	GT	AAG
(TTT)	 AG	4481-4581	GT	AGG
(CTC)	 AG	4907-4948	GT	AGG
-recovered pasa_asmbl_53548.p2, initial, 3683, 3722
-recovered pasa_asmbl_53548.p2, internal, 3885, 4015
-recovered pasa_asmbl_53548.p2, internal, 4271, 4388
-recovered pasa_asmbl_53548.p2, internal, 4481, 4581
-recovered pasa_asmbl_53548.p2, internal, 4907, 4948
Valid prediction for GlimmerHMM_glimmerT_21413-T1
Valid prediction for CodingQuarry_transcript_59963-T1
Valid prediction for snap_scaffold_8-snap.3405-T1
Valid prediction for Augustus_model.g14259.t1
Valid prediction for snap_scaffold_8-snap.3409-T1
Valid prediction for snap_scaffold_8-snap.3423-T1
Valid prediction for snap_scaffold_8-snap.3391-T1
Valid prediction for snap_scaffold_8-snap.3418-T1
Valid prediction for GlimmerHMM_glimmerT_21415-T1
Valid prediction for GlimmerHMM_glimmerT_21396-T1
Valid prediction for snap_scaffold_8-snap.3400-T1
Valid prediction for snap_scaffold_8-snap.3394-T1
Valid prediction for snap_scaffold_8-snap.3408-T1
Valid prediction for GlimmerHMM_glimmerT_21399-T1
Couldn't classify 113941, 114089
Couldn't classify 114616, 114751
Sorry, prediction pasa_asmbl_53562.p1 fails validation.
(AAC)	 AG	113941-114089	GT	AGG
(ACC)	 AG	114186-114270	GT	AGG
(GTG)	 AG	114346-114440	GT	AGG
(CAT)	 AG	114616-114751	TA	GGT
-recovered pasa_asmbl_53562.p1, internal, 113941, 114089
-recovered pasa_asmbl_53562.p1, internal, 114186, 114270
-recovered pasa_asmbl_53562.p1, internal, 114346, 114440
Valid prediction for GlimmerHMM_glimmerT_21384-T1
Couldn't classify 119762, 119926
Sorry, prediction pasa_asmbl_53563.p1 fails validation.
(AAT)	 AC	119762-119926	GT	AGG
(AAG)	 AG	121326-121518	GT	GGG
(AGG)	 AG	122460-122557	GT	AGG
(GAA)	 AG	122987-123100	AT	GAA
-recovered pasa_asmbl_53563.p1, terminal, 122987, 123100
-recovered pasa_asmbl_53563.p1, internal, 121326, 121518
-recovered pasa_asmbl_53563.p1, internal, 122460, 122557
Valid prediction for pasa_asmbl_53552.p1
Valid prediction for CodingQuarry_transcript_59965-T1
Valid prediction for CodingQuarry_transcript_59966-T1
Couldn't classify 96109, 96840
Sorry, prediction pasa_asmbl_53557.p1 fails validation.
(GCA)	 AC	96109-96840	TG	GAT
Valid prediction for GlimmerHMM_glimmerT_21397-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_21398-T1
Valid prediction for snap_scaffold_8-snap.3420-T1
Valid prediction for snap_scaffold_8-snap.3412-T1
Valid prediction for GlimmerHMM_glimmerT_21386-T1
Valid prediction for CodingQuarry_transcript_59970-T1
Valid prediction for HiQ_model.g14261.t1
Valid prediction for GlimmerHMM_glimmerT_21385-T1
Valid prediction for GlimmerHMM_glimmerT_21414-T1
Valid prediction for GlimmerHMM_glimmerT_21388-T1
Valid prediction for snap_scaffold_8-snap.3395-T1
Couldn't classify 59615, 60076
Sorry, prediction pasa_asmbl_52559.p1 fails validation.
(CTC)	 GG	59615-60076	AG	GAA
Couldn't classify 74959, 75097
Sorry, prediction pasa_asmbl_52555.p1 fails validation.
(CTC)	 AT	74959-75097	GT	AGG
(GTG)	 AG	75499-75683	AA	AAA
-recovered pasa_asmbl_52555.p1, terminal, 75499, 75683
Valid prediction for GlimmerHMM_glimmerT_21403-T1
Valid prediction for GlimmerHMM_glimmerT_21391-T1
Valid prediction for snap_scaffold_8-snap.3424-T1
Valid prediction for GlimmerHMM_glimmerT_21392-T1
Valid prediction for GlimmerHMM_glimmerT_21406-T1
Valid prediction for GlimmerHMM_glimmerT_21408-T1
Valid prediction for snap_scaffold_8-snap.3411-T1
Valid prediction for snap_scaffold_8-snap.3402-T1
Couldn't classify 82063, 82271
Sorry, prediction pasa_asmbl_52549.p1 fails validation.
(TTT)	 TC	82063-82271	GT	AGG
(GTA)	 AG	82380-82497	GT	AGG
(GTT)	 AG	85412-86500	AC	AAA
-recovered pasa_asmbl_52549.p1, terminal, 85412, 86500
-recovered pasa_asmbl_52549.p1, internal, 82380, 82497
Valid prediction for snap_scaffold_8-snap.3398-T1
Valid prediction for snap_scaffold_8-snap.3396-T1
Valid prediction for snap_scaffold_8-snap.3414-T1
Valid prediction for snap_scaffold_8-snap.3399-T1
Couldn't classify 56229, 56525
Sorry, prediction pasa_asmbl_52586.p1 fails validation.
(GTG)	 GT	56229-56525	GG	CTG
Valid prediction for Augustus_model.g14265.t1
Valid prediction for GlimmerHMM_glimmerT_21411-T1
Valid prediction for CodingQuarry_transcript_59971-T1
Valid prediction for snap_scaffold_8-snap.3416-T1
Valid prediction for GlimmerHMM_glimmerT_21409-T1
Valid prediction for snap_scaffold_8-snap.3419-T1
Valid prediction for GlimmerHMM_glimmerT_21390-T1
Valid prediction for snap_scaffold_8-snap.3403-T1
Valid prediction for pasa_asmbl_52557.p1
Valid prediction for GlimmerHMM_glimmerT_21394-T1
Valid prediction for snap_scaffold_8-snap.3410-T1
Valid prediction for GlimmerHMM_glimmerT_21401-T1
Valid prediction for snap_scaffold_8-snap.3415-T1
Valid prediction for GlimmerHMM_glimmerT_21389-T1
Couldn't classify 75499, 75665
Couldn't classify 76487, 76525
Sorry, prediction CodingQuarry_transcript_59969-T1 fails validation.
(ATG)	 AC	75040-75097	GT	AGG
(GTG)	 AG	75499-75665	GA	GTG
(TTT)	 GG	76487-76525	GG	AAG
-recovered CodingQuarry_transcript_59969-T1, initial, 75040, 75097
Valid prediction for GlimmerHMM_glimmerT_21404-T1
Valid prediction for GlimmerHMM_glimmerT_21410-T1
Couldn't classify 176399, 176520
Couldn't classify 182458, 182604
Sorry, prediction pasa_asmbl_52545.p1 fails validation.
(GTC)	 CA	176399-176520	GT	CGG
(CTC)	 AG	177551-177683	GT	AGG
(ACG)	 AG	178559-178712	GT	AGG
(GTG)	 AG	179320-179438	GT	AGG
(GTG)	 AG	179570-179635	GT	TGG
(GGT)	 AG	179855-180001	GT	AGG
(GAT)	 AG	182083-182364	GT	AGG
(GCG)	 AG	182458-182604	GT	AGG
-recovered pasa_asmbl_52545.p1, internal, 177551, 177683
-recovered pasa_asmbl_52545.p1, internal, 178559, 178712
-recovered pasa_asmbl_52545.p1, internal, 179320, 179438
-recovered pasa_asmbl_52545.p1, internal, 179570, 179635
-recovered pasa_asmbl_52545.p1, internal, 179855, 180001
-recovered pasa_asmbl_52545.p1, internal, 182083, 182364
-recovered pasa_asmbl_52545.p1, internal, 182458, 182604
Valid prediction for GlimmerHMM_glimmerT_21407-T1
Valid prediction for snap_scaffold_8-snap.3417-T1
Valid prediction for snap_scaffold_8-snap.3397-T1
Valid prediction for pasa_asmbl_52542.p1
Couldn't classify 1291, 1639
Sorry, prediction GlimmerHMM_glimmerT_21417-T1 fails validation.
(TTC)	 AG	1291-1639	GT	GCG
(CCA)	 AG	1784-1963	GG	AGG
-recovered GlimmerHMM_glimmerT_21417-T1, terminal, 1784, 1963
-recovered GlimmerHMM_glimmerT_21417-T1, internal, 1291, 1639
Valid prediction for snap_scaffold_8-snap.3401-T1
Valid prediction for Augustus_model.g14263.t1
Valid prediction for Augustus_model.g14262.t1
Valid prediction for GlimmerHMM_glimmerT_21387-T1
Valid prediction for Augustus_model.g14264.t1
Valid prediction for Augustus_model.g14266.t1

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

-building trellis in range 1 - 217708
-exon list size: 311


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.6    
2.9    
3.2    
3.5    
3.8    
4.2    
4.5    
4.8    
5.1    
5.4    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.7    
8.0    
8.3    
8.6    
8.9    
9.3    
9.6    
9.9    
10.2    
10.5    
10.9    
11.2    
11.5    
11.8    
12.1    
12.5    
12.8    
13.1    
13.4    
13.7    
14.1    
14.4    
14.7    
15.0    
15.3    
15.7    
16.0    
16.3    
16.6    
16.9    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.2    
19.5    
19.8    
20.1    
20.4    
20.8    
21.1    
21.4    
21.7    
22.0    
22.4    
22.7    
23.0    
23.3    
23.6    
24.0    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.8    
27.2    
27.5    
27.8    
28.1    
28.4    
28.8    
29.1    
29.4    
29.7    
30.0    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.5    
35.8    
36.1    
36.4    
36.7    
37.1    
37.4    
37.7    
38.0    
38.3    
38.7    
39.0    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.2    
41.5    
41.9    
42.2    
42.5    
42.8    
43.1    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.4    
45.7    
46.0    
46.3    
46.6    
47.0    
47.3    
47.6    
47.9    
48.2    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.8    
52.1    
52.4    
52.7    
53.0    
53.4    
53.7    
54.0    
54.3    
54.6    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.9    
57.2    
57.5    
57.8    
58.1    
58.5    
58.8    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.0    
61.3    
61.7    
62.0    
62.3    
62.6    
62.9    
63.3    
63.6    
63.9    
64.2    
64.5    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
70.0    
70.3    
70.6    
70.9    
71.2    
71.6    
71.9    
72.2    
72.5    
72.8    
73.2    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.0    
76.4    
76.7    
77.0    
77.3    
77.6    
78.0    
78.3    
78.6    
78.9    
79.2    
79.6    
79.9    
80.2    
80.5    
80.8    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.1    
83.4    
83.7    
84.0    
84.3    
84.7    
85.0    
85.3    
85.6    
85.9    
86.3    
86.6    
86.9    
87.2    
87.5    
87.9    
88.2    
88.5    
88.8    
89.1    
89.5    
89.8    
90.1    
90.4    
90.7    
91.1    
91.4    
91.7    
92.0    
92.3    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.6    
94.9    
95.2    
95.5    
95.8    
96.2    
96.5    
96.8    
97.1    
97.4    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 32 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support