-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_7546735-7841503

-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.6775_t
Valid prediction for GeneMark_model.6782_t
Valid prediction for Augustus_model.g2832.t1
Valid prediction for snap_scaffold_2-snap.1636-T1
Valid prediction for GlimmerHMM_glimmerT_4198-T1
Valid prediction for GeneMark_model.6780_t
Valid prediction for GlimmerHMM_glimmerT_4211-T1
Valid prediction for snap_scaffold_2-snap.1623-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_4197-T1
Valid prediction for GeneMark_model.6786_t
Valid prediction for GeneMark_model.6794_t
Valid prediction for Augustus_model.g2831.t1
Valid prediction for GlimmerHMM_glimmerT_4199-T1
Valid prediction for CodingQuarry_transcript_28550-T1
Valid prediction for GlimmerHMM_glimmerT_4206-T1
Valid prediction for snap_scaffold_2-snap.1642-T1
Valid prediction for GeneMark_model.6792_t
Valid prediction for snap_scaffold_2-snap.1641-T1
Valid prediction for HiQ_model.g2829.t1
Valid prediction for CodingQuarry_transcript_28553-T1
Valid prediction for Augustus_model.g2826.t1
Valid prediction for snap_scaffold_2-snap.1639-T1
Valid prediction for snap_scaffold_2-snap.1645-T1
Valid prediction for snap_scaffold_2-snap.1633-T1
Valid prediction for snap_scaffold_2-snap.1616-T1
Valid prediction for GlimmerHMM_glimmerT_4216-T1
Valid prediction for snap_scaffold_2-snap.1618-T1
Valid prediction for snap_scaffold_2-snap.1644-T1
Valid prediction for snap_scaffold_2-snap.1648-T1
Valid prediction for snap_scaffold_2-snap.1637-T1
Valid prediction for GeneMark_model.6789_t
Valid prediction for GlimmerHMM_glimmerT_4212-T1
Valid prediction for snap_scaffold_2-snap.1631-T1
Valid prediction for GlimmerHMM_glimmerT_4196-T1
Valid prediction for Augustus_model.g2823.t1
Valid prediction for snap_scaffold_2-snap.1630-T1
Valid prediction for GlimmerHMM_glimmerT_4203-T1
Valid prediction for GeneMark_model.6781_t
Valid prediction for Augustus_model.g2833.t1
Valid prediction for GeneMark_model.6773_t
Valid prediction for CodingQuarry_transcript_28551-T1
Valid prediction for GeneMark_model.6777_t
Couldn't classify 233588, 233721
Sorry, prediction pasa_asmbl_24613.p2 fails validation.
(GCT)	 AG	233588-233721	GT	AGG
(AGG)	 AG	234181-234298	GC	AGG
(GTT)	 AG	234541-234611	GT	GGG
(CAA)	 AG	235385-235460	GT	AGG
(TAC)	 AG	235734-235796	GC	AGG
(GCT)	 AG	235886-235955	GT	AGG
(ATG)	 AG	236367-236449	TT	AAT
-recovered pasa_asmbl_24613.p2, terminal, 236367, 236449
-recovered pasa_asmbl_24613.p2, internal, 233588, 233721
-recovered pasa_asmbl_24613.p2, internal, 234181, 234298
-recovered pasa_asmbl_24613.p2, internal, 234541, 234611
-recovered pasa_asmbl_24613.p2, internal, 235385, 235460
-recovered pasa_asmbl_24613.p2, internal, 235734, 235796
-recovered pasa_asmbl_24613.p2, internal, 235886, 235955
Valid prediction for GlimmerHMM_glimmerT_4207-T1
Valid prediction for snap_scaffold_2-snap.1640-T1
Valid prediction for CodingQuarry_transcript_28555-T1
Valid prediction for CodingQuarry_transcript_28554-T1
Valid prediction for Augustus_model.g2828.t1
Valid prediction for snap_scaffold_2-snap.1620-T1
Valid prediction for CodingQuarry_transcript_28552-T1
Valid prediction for GlimmerHMM_glimmerT_4213-T1
Valid prediction for snap_scaffold_2-snap.1617-T1
Valid prediction for pasa_asmbl_24616.p1
Valid prediction for snap_scaffold_2-snap.1621-T1
Valid prediction for snap_scaffold_2-snap.1635-T1
Valid prediction for GlimmerHMM_glimmerT_4204-T1
Valid prediction for snap_scaffold_2-snap.1638-T1
Valid prediction for GlimmerHMM_glimmerT_4214-T1
Valid prediction for GeneMark_model.6793_t
Valid prediction for GeneMark_model.6791_t
Valid prediction for GeneMark_model.6790_t
Valid prediction for HiQ_model.g2830.t1
Valid prediction for HiQ_model.g2835.t1
Valid prediction for GlimmerHMM_glimmerT_4201-T1
Valid prediction for snap_scaffold_2-snap.1629-T1
Valid prediction for Augustus_model.g2822.t1
Valid prediction for snap_scaffold_2-snap.1634-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 Augustus_model.g2825.t1
Valid prediction for Augustus_model.g2836.t1
Valid prediction for snap_scaffold_2-snap.1624-T1
Valid prediction for HiQ_model.g2834.t1
Valid prediction for Augustus_model.g2821.t1
Valid prediction for snap_scaffold_2-snap.1628-T1
Valid prediction for CodingQuarry_transcript_28556-T1
Valid prediction for Augustus_model.g2837.t1
Valid prediction for GeneMark_model.6796_t
Valid prediction for snap_scaffold_2-snap.1627-T1
Valid prediction for GeneMark_model.6788_t
Valid prediction for GeneMark_model.6774_t
Valid prediction for snap_scaffold_2-snap.1647-T1
Valid prediction for GlimmerHMM_glimmerT_4209-T1
Valid prediction for GlimmerHMM_glimmerT_4208-T1
Valid prediction for GlimmerHMM_glimmerT_4217-T1
Couldn't classify 170362, 170721
Sorry, prediction pasa_asmbl_23296.p1 fails validation.
(ATC)	 TG	170362-170721	CA	TCC
Couldn't classify 12967, 13014
Sorry, prediction pasa_asmbl_23307.p1 fails validation.
(CCT)	 CA	12967-13014	GT	TGG
(GTG)	 AG	13310-13501	GT	AGG
(GAC)	 AG	14136-14184	GT	AGG
(AGA)	 AG	14388-14491	TC	AAT
-recovered pasa_asmbl_23307.p1, terminal, 14388, 14491
-recovered pasa_asmbl_23307.p1, internal, 13310, 13501
-recovered pasa_asmbl_23307.p1, internal, 14136, 14184
Valid prediction for GlimmerHMM_glimmerT_4205-T1
Valid prediction for snap_scaffold_2-snap.1626-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.6784_t
Valid prediction for Augustus_model.g2819.t1
Couldn't classify 1321, 1440
Couldn't classify 7744, 7893
Sorry, prediction pasa_asmbl_23308.p1 fails validation.
(CTC)	 CC	1321-1440	GT	TGG
(CTC)	 AG	2807-3036	GT	AGG
(CTA)	 AG	4627-4782	GT	CGG
(CTC)	 AG	6140-6377	GT	AGG
(TCT)	 AG	7744-7893	GT	AGG
-recovered pasa_asmbl_23308.p1, internal, 2807, 3036
-recovered pasa_asmbl_23308.p1, internal, 4627, 4782
-recovered pasa_asmbl_23308.p1, internal, 6140, 6377
-recovered pasa_asmbl_23308.p1, internal, 7744, 7893
Valid prediction for snap_scaffold_2-snap.1622-T1
Valid prediction for GeneMark_model.6776_t
Valid prediction for GeneMark_model.6779_t
Valid prediction for GlimmerHMM_glimmerT_4200-T1
Valid prediction for Augustus_model.g2824.t1
Valid prediction for snap_scaffold_2-snap.1649-T1
Valid prediction for Augustus_model.g2820.t1
Valid prediction for GeneMark_model.6787_t
Valid prediction for snap_scaffold_2-snap.1643-T1
Valid prediction for GeneMark_model.6795_t
Valid prediction for CodingQuarry_transcript_28557-T1
Valid prediction for Augustus_model.g2827.t1
Valid prediction for snap_scaffold_2-snap.1619-T1
Valid prediction for GlimmerHMM_glimmerT_4215-T1
Valid prediction for GlimmerHMM_glimmerT_4202-T1
Valid prediction for GeneMark_model.6778_t
Valid prediction for GeneMark_model.6785_t
Valid prediction for GlimmerHMM_glimmerT_4210-T1
Valid prediction for snap_scaffold_2-snap.1625-T1
Valid prediction for snap_scaffold_2-snap.1646-T1
Valid prediction for snap_scaffold_2-snap.1632-T1
Valid prediction for pasa_asmbl_23300.p1

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

-building trellis in range 1 - 294769
-exon list size: 433


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.4    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.7    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.4    
7.6    
7.8    
8.0    
8.3    
8.5    
8.7    
9.0    
9.2    
9.4    
9.7    
9.9    
10.1    
10.3    
10.6    
10.8    
11.0    
11.3    
11.5    
11.7    
12.0    
12.2    
12.4    
12.6    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.3    
14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.0    
17.2    
17.5    
17.7    
17.9    
18.2    
18.4    
18.6    
18.9    
19.1    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.4    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.4    
29.7    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.3    
31.5    
31.7    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.1    
41.4    
41.6    
41.8    
42.1    
42.3    
42.5    
42.8    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
54.9    
55.2    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.0    
57.2    
57.5    
57.7    
57.9    
58.2    
58.4    
58.6    
58.9    
59.1    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.1    
62.3    
62.5    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.0    
68.3    
68.5    
68.7    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.3    
70.6    
70.8    
71.0    
71.3    
71.5    
71.7    
72.0    
72.2    
72.4    
72.6    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.0    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 22 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 34873
-exon list size: 32


building trellis

2.9    
5.9    
8.8    
11.8    
14.7    
17.6    
20.6    
23.5    
26.5    
29.4    
32.4    
35.3    
38.2    
41.2    
44.1    
47.1    
50.0    
52.9    
55.9    
58.8    
61.8    
64.7    
67.6    
70.6    
73.5    
76.5    
79.4    
82.4    
85.3    
88.2    
91.2    
94.1    
97.1    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13677
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1857 - 13677
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 13778 - 34873
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 13778 - 29365
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 13778 - 29128
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 16677 - 29128
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 17226 - 29128
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support