-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_13944217-14099227

-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_7846-T1
Valid prediction for snap_scaffold_3-snap.2703-T1
Valid prediction for GeneMark_model.12839_t
Valid prediction for GlimmerHMM_glimmerT_7858-T1
Valid prediction for GeneMark_model.12840_t
Valid prediction for GlimmerHMM_glimmerT_7848-T1
Valid prediction for HiQ_model.g5186.t1
Valid prediction for Augustus_model.g5200.t1
Valid prediction for Augustus_model.g5185.t1
Valid prediction for GlimmerHMM_glimmerT_7861-T1
Valid prediction for Augustus_model.g5187.t1
Valid prediction for GeneMark_model.12843_t
Valid prediction for snap_scaffold_3-snap.2688-T1
Valid prediction for Augustus_model.g5198.t1
Valid prediction for snap_scaffold_3-snap.2704-T1
Valid prediction for CodingQuarry_transcript_46237-T1
Valid prediction for GlimmerHMM_glimmerT_7854-T1
Valid prediction for GlimmerHMM_glimmerT_7856-T1
Valid prediction for GeneMark_model.12845_t
Valid prediction for GlimmerHMM_glimmerT_7851-T1
Valid prediction for snap_scaffold_3-snap.2707-T1
Valid prediction for GeneMark_model.12844_t
Valid prediction for GeneMark_model.12833_t
Valid prediction for Augustus_model.g5191.t1
Valid prediction for snap_scaffold_3-snap.2693-T1
Valid prediction for Augustus_model.g5196.t1
Couldn't classify 75570, 75641
Sorry, prediction pasa_asmbl_40453.p1 fails validation.
(ATG)	 TG	70111-70182	GT	AGG
(ATG)	 AG	72401-72528	GT	CGG
(CCA)	 AG	72708-72879	GT	TGG
(ATG)	 AG	74907-75107	GT	AGG
(ACC)	 AG	75570-75641	AA	GCA
-recovered pasa_asmbl_40453.p1, initial, 70111, 70182
-recovered pasa_asmbl_40453.p1, initial, 72401, 72528
-recovered pasa_asmbl_40453.p1, initial, 74907, 75107
-recovered pasa_asmbl_40453.p1, internal, 72401, 72528
-recovered pasa_asmbl_40453.p1, internal, 72708, 72879
-recovered pasa_asmbl_40453.p1, internal, 74907, 75107
Couldn't classify 125001, 125315
Sorry, prediction pasa_asmbl_40459.p1 fails validation.
(ATG)	 AG	125001-125315	AA	ACA
Valid prediction for GlimmerHMM_glimmerT_7844-T1
Valid prediction for Augustus_model.g5189.t1
Valid prediction for snap_scaffold_3-snap.2696-T1
Valid prediction for GlimmerHMM_glimmerT_7852-T1
Valid prediction for Augustus_model.g5199.t1
Valid prediction for GeneMark_model.12835_t
Couldn't classify 61892, 61933
Sorry, prediction pasa_asmbl_40446.p1 fails validation.
(GCG)	 TG	61892-61933	GT	AGG
(TGT)	 AG	62681-62777	GT	GGG
(TTA)	 AG	65747-67291	GT	GGG
(AAG)	 AG	69453-69622	GA	GAG
-recovered pasa_asmbl_40446.p1, terminal, 69453, 69622
-recovered pasa_asmbl_40446.p1, internal, 62681, 62777
-recovered pasa_asmbl_40446.p1, internal, 65747, 67291
Valid prediction for CodingQuarry_transcript_46236-T1
Valid prediction for GeneMark_model.12842_t
Valid prediction for snap_scaffold_3-snap.2702-T1
Valid prediction for GeneMark_model.12836_t
Valid prediction for snap_scaffold_3-snap.2691-T1
Valid prediction for Augustus_model.g5184.t1
Valid prediction for GlimmerHMM_glimmerT_7850-T1
Valid prediction for snap_scaffold_3-snap.2684-T1
Valid prediction for Augustus_model.g5188.t1
Valid prediction for Augustus_model.g5192.t1
Valid prediction for GlimmerHMM_glimmerT_7859-T1
Valid prediction for GeneMark_model.12837_t
Valid prediction for GeneMark_model.12834_t
Valid prediction for Augustus_model.g5197.t1
Valid prediction for snap_scaffold_3-snap.2687-T1
Valid prediction for Augustus_model.g5179.t1
Valid prediction for snap_scaffold_3-snap.2708-T1
Valid prediction for snap_scaffold_3-snap.2690-T1
Valid prediction for GeneMark_model.12846_t
Valid prediction for snap_scaffold_3-snap.2698-T1
Couldn't classify 48990, 49113
Sorry, prediction pasa_asmbl_40434.p1 fails validation.
(ATG)	 AG	44889-44933	GT	AGG
(TGT)	 AG	45358-45460	GT	AAG
(AAA)	 AG	46455-47279	GT	GGG
(CTC)	 AG	48850-48913	GT	CAG
(GGC)	 AG	48990-49113	GG	CAG
-recovered pasa_asmbl_40434.p1, initial, 44889, 44933
-recovered pasa_asmbl_40434.p1, internal, 44889, 44933
-recovered pasa_asmbl_40434.p1, internal, 45358, 45460
-recovered pasa_asmbl_40434.p1, internal, 46455, 47279
-recovered pasa_asmbl_40434.p1, internal, 48850, 48913

-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 snap_scaffold_3-snap.2697-T1
Valid prediction for snap_scaffold_3-snap.2682-T1
Valid prediction for GeneMark_model.12830_t
Valid prediction for Augustus_model.g5182.t1
Valid prediction for Augustus_model.g5194.t1
Valid prediction for Augustus_model.g5181.t1
Valid prediction for snap_scaffold_3-snap.2706-T1
Valid prediction for GlimmerHMM_glimmerT_7863-T1
Valid prediction for GlimmerHMM_glimmerT_7845-T1
Valid prediction for snap_scaffold_3-snap.2695-T1
Valid prediction for GlimmerHMM_glimmerT_7855-T1
Valid prediction for Augustus_model.g5193.t1
Valid prediction for GeneMark_model.12828_t
Valid prediction for Augustus_model.g5190.t1
Valid prediction for snap_scaffold_3-snap.2681-T1
Valid prediction for snap_scaffold_3-snap.2683-T1
Valid prediction for GeneMark_model.12829_t
Valid prediction for snap_scaffold_3-snap.2705-T1
Valid prediction for Augustus_model.g5180.t1
Valid prediction for snap_scaffold_3-snap.2689-T1
Valid prediction for GeneMark_model.12832_t
Valid prediction for Augustus_model.g5195.t1
Valid prediction for HiQ_model.g5183.t1
Valid prediction for GlimmerHMM_glimmerT_7847-T1
Valid prediction for GeneMark_model.12847_t
Valid prediction for pasa_asmbl_39265.p1
Valid prediction for GlimmerHMM_glimmerT_7853-T1
Valid prediction for snap_scaffold_3-snap.2701-T1
Valid prediction for snap_scaffold_3-snap.2692-T1
Valid prediction for snap_scaffold_3-snap.2700-T1
Valid prediction for GlimmerHMM_glimmerT_7843-T1
Valid prediction for GlimmerHMM_glimmerT_7862-T1
Valid prediction for snap_scaffold_3-snap.2686-T1
Valid prediction for snap_scaffold_3-snap.2694-T1
Valid prediction for Augustus_model.g5202.t1
Valid prediction for snap_scaffold_3-snap.2685-T1
Valid prediction for GeneMark_model.12841_t
Valid prediction for Augustus_model.g5178.t1
Valid prediction for GlimmerHMM_glimmerT_7849-T1
Valid prediction for snap_scaffold_3-snap.2699-T1
Valid prediction for GlimmerHMM_glimmerT_7860-T1
Couldn't classify 113054, 113167
Sorry, prediction pasa_asmbl_39268.p1 fails validation.
(ATG)	 CT	112099-112181	GT	AGG
(AGA)	 AG	112322-112390	GT	GGG
(GCA)	 AG	112601-112747	GT	AGG
(GTG)	 AG	112823-112979	GT	TGG
(ACA)	 AG	113054-113167	TA	AGT
-recovered pasa_asmbl_39268.p1, initial, 112099, 112181
-recovered pasa_asmbl_39268.p1, internal, 112322, 112390
-recovered pasa_asmbl_39268.p1, internal, 112601, 112747
-recovered pasa_asmbl_39268.p1, internal, 112823, 112979
Valid prediction for Augustus_model.g5201.t1
Valid prediction for GlimmerHMM_glimmerT_7857-T1

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

-building trellis in range 1 - 155011
-exon list size: 275


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.2    
2.5    
2.9    
3.2    
3.6    
4.0    
4.3    
4.7    
5.1    
5.4    
5.8    
6.1    
6.5    
6.9    
7.2    
7.6    
7.9    
8.3    
8.7    
9.0    
9.4    
9.7    
10.1    
10.5    
10.8    
11.2    
11.6    
11.9    
12.3    
12.6    
13.0    
13.4    
13.7    
14.1    
14.4    
14.8    
15.2    
15.5    
15.9    
16.2    
16.6    
17.0    
17.3    
17.7    
18.1    
18.4    
18.8    
19.1    
19.5    
19.9    
20.2    
20.6    
20.9    
21.3    
21.7    
22.0    
22.4    
22.7    
23.1    
23.5    
23.8    
24.2    
24.5    
24.9    
25.3    
25.6    
26.0    
26.4    
26.7    
27.1    
27.4    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
30.0    
30.3    
30.7    
31.0    
31.4    
31.8    
32.1    
32.5    
32.9    
33.2    
33.6    
33.9    
34.3    
34.7    
35.0    
35.4    
35.7    
36.1    
36.5    
36.8    
37.2    
37.5    
37.9    
38.3    
38.6    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.2    
41.5    
41.9    
42.2    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.8    
45.1    
45.5    
45.8    
46.2    
46.6    
46.9    
47.3    
47.7    
48.0    
48.4    
48.7    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.3    
51.6    
52.0    
52.3    
52.7    
53.1    
53.4    
53.8    
54.2    
54.5    
54.9    
55.2    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.8    
58.1    
58.5    
58.8    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.4    
61.7    
62.1    
62.5    
62.8    
63.2    
63.5    
63.9    
64.3    
64.6    
65.0    
65.3    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.9    
68.2    
68.6    
69.0    
69.3    
69.7    
70.0    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.6    
72.9    
73.3    
73.6    
74.0    
74.4    
74.7    
75.1    
75.5    
75.8    
76.2    
76.5    
76.9    
77.3    
77.6    
78.0    
78.3    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.9    
81.2    
81.6    
81.9    
82.3    
82.7    
83.0    
83.4    
83.8    
84.1    
84.5    
84.8    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.4    
87.7    
88.1    
88.4    
88.8    
89.2    
89.5    
89.9    
90.3    
90.6    
91.0    
91.3    
91.7    
92.1    
92.4    
92.8    
93.1    
93.5    
93.9    
94.2    
94.6    
94.9    
95.3    
95.7    
96.0    
96.4    
96.8    
97.1    
97.5    
97.8    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 27 predictions from path traversal
GOT 5prime partial gene.

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