-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_13526614-13741464

-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.12777_t
Valid prediction for GeneMark_model.12783_t
Valid prediction for Augustus_model.g5142.t1
Valid prediction for GlimmerHMM_glimmerT_7801-T1
Valid prediction for Augustus_model.g5138.t1
Couldn't classify 91074, 91220
Couldn't classify 92394, 92475
Sorry, prediction pasa_asmbl_40815.p1 fails validation.
(GGG)	 CA	91074-91220	GT	AGG
(ATT)	 AG	91692-91778	GT	AGG
(AGC)	 AG	91871-91929	GT	AGG
(ACT)	 AG	92394-92475	GT	AGG
add_exon() Sorry, pasa_asmbl_40815.p1 91871-91929-terminal-2 is invalid.
-recovered pasa_asmbl_40815.p1, terminal, 91871, 91929
-recovered pasa_asmbl_40815.p1, internal, 91692, 91778
-recovered pasa_asmbl_40815.p1, internal, 91871, 91929
-recovered pasa_asmbl_40815.p1, internal, 92394, 92475
Valid prediction for GlimmerHMM_glimmerT_7771-T1
Couldn't classify 48252, 48554
Sorry, prediction pasa_asmbl_40818.p1 fails validation.
(TTT)	 TG	48252-48554	CC	GCC
Valid prediction for snap_scaffold_3-snap.2615-T1
Valid prediction for GlimmerHMM_glimmerT_7769-T1
Valid prediction for snap_scaffold_3-snap.2637-T1
Valid prediction for GlimmerHMM_glimmerT_7767-T1
Valid prediction for GlimmerHMM_glimmerT_7780-T1
Valid prediction for GeneMark_model.12779_t
Valid prediction for Augustus_model.g5128.t1
Valid prediction for snap_scaffold_3-snap.2614-T1
Valid prediction for GlimmerHMM_glimmerT_7788-T1
Valid prediction for snap_scaffold_3-snap.2611-T1
Valid prediction for GeneMark_model.12795_t
Valid prediction for GeneMark_model.12801_t
Valid prediction for GeneMark_model.12780_t
Valid prediction for HiQ_model.g5143.t1
Valid prediction for Augustus_model.g5126.t1
Valid prediction for GeneMark_model.12788_t
Valid prediction for GlimmerHMM_glimmerT_7790-T1
Valid prediction for snap_scaffold_3-snap.2616-T1
Valid prediction for GeneMark_model.12796_t
Valid prediction for snap_scaffold_3-snap.2617-T1
Valid prediction for GlimmerHMM_glimmerT_7798-T1
Valid prediction for CodingQuarry_transcript_46224-T1
Valid prediction for Augustus_model.g5141.t1
Valid prediction for GlimmerHMM_glimmerT_7782-T1
Valid prediction for Augustus_model.g5120.t1
Valid prediction for GlimmerHMM_glimmerT_7791-T1
Valid prediction for Augustus_model.g5124.t1
Valid prediction for Augustus_model.g5118.t1
Valid prediction for snap_scaffold_3-snap.2639-T1
Valid prediction for GeneMark_model.12784_t
Valid prediction for GlimmerHMM_glimmerT_7766-T1
Valid prediction for GlimmerHMM_glimmerT_7797-T1
Valid prediction for GeneMark_model.12774_t
Valid prediction for GlimmerHMM_glimmerT_7792-T1
Valid prediction for GeneMark_model.12790_t
Valid prediction for GlimmerHMM_glimmerT_7793-T1
Valid prediction for snap_scaffold_3-snap.2638-T1
Valid prediction for snap_scaffold_3-snap.2624-T1
Valid prediction for GeneMark_model.12791_t
Valid prediction for GlimmerHMM_glimmerT_7770-T1
Valid prediction for GeneMark_model.12781_t
Valid prediction for GlimmerHMM_glimmerT_7777-T1
Valid prediction for HiQ_model.g5144.t1
Valid prediction for CodingQuarry_transcript_46225-T1
Valid prediction for GlimmerHMM_glimmerT_7799-T1
Valid prediction for snap_scaffold_3-snap.2636-T1
Valid prediction for Augustus_model.g5135.t1
Valid prediction for GlimmerHMM_glimmerT_7796-T1
Valid prediction for GlimmerHMM_glimmerT_7783-T1
Valid prediction for snap_scaffold_3-snap.2627-T1
Valid prediction for snap_scaffold_3-snap.2628-T1
Valid prediction for snap_scaffold_3-snap.2613-T1
Valid prediction for snap_scaffold_3-snap.2618-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7773-T1
Valid prediction for pasa_asmbl_40409.p1
Valid prediction for snap_scaffold_3-snap.2631-T1
Valid prediction for GeneMark_model.12772_t
Valid prediction for Augustus_model.g5129.t1
Valid prediction for Augustus_model.g5122.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 snap_scaffold_3-snap.2619-T1
Valid prediction for Augustus_model.g5132.t1
Valid prediction for GeneMark_model.12799_t
Couldn't classify 75478, 75552
Couldn't classify 77113, 77177
Sorry, prediction pasa_asmbl_39231.p1 fails validation.
(CAT)	 AG	75478-75552	GT	AGG
(AGC)	 AG	76527-76655	GT	CGG
(GGA)	 AG	76787-76877	GT	AGG
(CTC)	 AG	77113-77177	AT	GTA
-recovered pasa_asmbl_39231.p1, internal, 75478, 75552
-recovered pasa_asmbl_39231.p1, internal, 76527, 76655
-recovered pasa_asmbl_39231.p1, internal, 76787, 76877
Valid prediction for Augustus_model.g5123.t1
Valid prediction for Augustus_model.g5131.t1
Valid prediction for GlimmerHMM_glimmerT_7772-T1
Valid prediction for GlimmerHMM_glimmerT_7785-T1
Valid prediction for Augustus_model.g5116.t1
Valid prediction for GlimmerHMM_glimmerT_7776-T1
Valid prediction for GeneMark_model.12794_t
Valid prediction for snap_scaffold_3-snap.2644-T1
Valid prediction for GlimmerHMM_glimmerT_7778-T1
Valid prediction for Augustus_model.g5134.t1
Valid prediction for GeneMark_model.12793_t
Valid prediction for Augustus_model.g5133.t1
Valid prediction for snap_scaffold_3-snap.2632-T1
Valid prediction for GeneMark_model.12771_t
Valid prediction for snap_scaffold_3-snap.2634-T1
Valid prediction for snap_scaffold_3-snap.2633-T1
Valid prediction for Augustus_model.g5127.t1
Valid prediction for CodingQuarry_transcript_46223-T1
Valid prediction for Augustus_model.g5145.t1
Valid prediction for GlimmerHMM_glimmerT_7800-T1
Valid prediction for snap_scaffold_3-snap.2626-T1
Valid prediction for snap_scaffold_3-snap.2620-T1
Valid prediction for Augustus_model.g5136.t1
Valid prediction for Augustus_model.g5121.t1
Valid prediction for GeneMark_model.12776_t
Valid prediction for Augustus_model.g5130.t1
Valid prediction for GlimmerHMM_glimmerT_7804-T1
Valid prediction for HiQ_model.g5117.t1
Valid prediction for pasa_asmbl_39242.p1
Valid prediction for HiQ_model.g5137.t1
Valid prediction for snap_scaffold_3-snap.2612-T1
Valid prediction for GlimmerHMM_glimmerT_7784-T1
Valid prediction for snap_scaffold_3-snap.2623-T1
Valid prediction for GlimmerHMM_glimmerT_7775-T1
Valid prediction for snap_scaffold_3-snap.2630-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2642-T1
Valid prediction for snap_scaffold_3-snap.2641-T1
Couldn't classify 64073, 64172
Sorry, prediction pasa_asmbl_39235.p1 fails validation.
(AGT)	 AG	64073-64172	GT	TGG
(AGA)	 AG	64523-64601	GT	AGG
(TGG)	 AG	65747-65882	GT	AGG
(GTT)	 AG	65969-66049	GG	GAG
-recovered pasa_asmbl_39235.p1, terminal, 65969, 66049
-recovered pasa_asmbl_39235.p1, internal, 64073, 64172
-recovered pasa_asmbl_39235.p1, internal, 64523, 64601
-recovered pasa_asmbl_39235.p1, internal, 65747, 65882
Valid prediction for GlimmerHMM_glimmerT_7786-T1
Valid prediction for GlimmerHMM_glimmerT_7781-T1
Valid prediction for GlimmerHMM_glimmerT_7779-T1
Valid prediction for GlimmerHMM_glimmerT_7787-T1
Valid prediction for Augustus_model.g5146.t1
Valid prediction for GlimmerHMM_glimmerT_7768-T1
Valid prediction for GeneMark_model.12798_t
Valid prediction for CodingQuarry_transcript_46226-T1
Valid prediction for snap_scaffold_3-snap.2629-T1
Valid prediction for GeneMark_model.12773_t
Valid prediction for GeneMark_model.12789_t
Valid prediction for GeneMark_model.12786_t
Valid prediction for Augustus_model.g5139.t1
Valid prediction for Augustus_model.g5119.t1
Valid prediction for Augustus_model.g5114.t1
Valid prediction for GeneMark_model.12797_t
Valid prediction for Augustus_model.g5115.t1
Valid prediction for GeneMark_model.12787_t
Valid prediction for GlimmerHMM_glimmerT_7802-T1
Valid prediction for Augustus_model.g5125.t1
Valid prediction for GlimmerHMM_glimmerT_7789-T1
Valid prediction for GlimmerHMM_glimmerT_7795-T1
Valid prediction for snap_scaffold_3-snap.2621-T1
Valid prediction for GlimmerHMM_glimmerT_7774-T1
Valid prediction for Augustus_model.g5140.t1
Valid prediction for snap_scaffold_3-snap.2640-T1
Valid prediction for GeneMark_model.12782_t
Valid prediction for GeneMark_model.12800_t
Valid prediction for GlimmerHMM_glimmerT_7803-T1
Valid prediction for GeneMark_model.12775_t
Valid prediction for snap_scaffold_3-snap.2625-T1
Valid prediction for GeneMark_model.12778_t
Valid prediction for snap_scaffold_3-snap.2643-T1
Valid prediction for Augustus_model.g5148.t1
Valid prediction for snap_scaffold_3-snap.2635-T1
Valid prediction for HiQ_model.g5147.t1
Valid prediction for GlimmerHMM_glimmerT_7765-T1
Valid prediction for snap_scaffold_3-snap.2610-T1
Valid prediction for GlimmerHMM_glimmerT_7794-T1
Valid prediction for snap_scaffold_3-snap.2622-T1
Valid prediction for snap_scaffold_3-snap.2609-T1
Valid prediction for GeneMark_model.12785_t

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

-building trellis in range 1 - 214851
-exon list size: 377


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
4.2    
4.5    
4.7    
5.0    
5.3    
5.5    
5.8    
6.1    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.0    
10.3    
10.6    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.8    
16.1    
16.4    
16.6    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.5    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.4    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.1    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.5    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.4    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
90.0    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 39 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support