-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_16634830-16813126

-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 Augustus_model.g21062.t1
Valid prediction for GlimmerHMM_glimmerT_31524-T1
Valid prediction for GeneMark_model.54324_t
Valid prediction for snap_scaffold_12-snap.3229-T1
Valid prediction for GeneMark_model.54332_t
Valid prediction for Augustus_model.g21052.t1
Valid prediction for snap_scaffold_12-snap.3241-T1
Valid prediction for GeneMark_model.54328_t
Valid prediction for GlimmerHMM_glimmerT_31537-T1
Valid prediction for GeneMark_model.54344_t
Valid prediction for Augustus_model.g21069.t1
Valid prediction for Augustus_model.g21048.t1
Valid prediction for snap_scaffold_12-snap.3233-T1
Valid prediction for GeneMark_model.54343_t
Valid prediction for GlimmerHMM_glimmerT_31531-T1
Valid prediction for Augustus_model.g21060.t1
Valid prediction for GlimmerHMM_glimmerT_31520-T1
Valid prediction for GlimmerHMM_glimmerT_31518-T1
Valid prediction for snap_scaffold_12-snap.3228-T1
Valid prediction for snap_scaffold_12-snap.3234-T1
Valid prediction for snap_scaffold_12-snap.3248-T1
Valid prediction for GlimmerHMM_glimmerT_31522-T1
Valid prediction for GeneMark_model.54333_t
Valid prediction for GlimmerHMM_glimmerT_31521-T1
Couldn't classify 53564, 53995
Sorry, prediction pasa_asmbl_8274.p1 fails validation.
(ATG)	 CC	53564-53995	AT	GCA
Valid prediction for Augustus_model.g21050.t1
Valid prediction for snap_scaffold_12-snap.3237-T1
Valid prediction for snap_scaffold_12-snap.3230-T1
Valid prediction for snap_scaffold_12-snap.3227-T1
Valid prediction for snap_scaffold_12-snap.3240-T1
Valid prediction for GeneMark_model.54346_t
Valid prediction for GeneMark_model.54331_t
Valid prediction for Augustus_model.g21061.t1
Valid prediction for Augustus_model.g21054.t1
Valid prediction for snap_scaffold_12-snap.3225-T1
Valid prediction for GlimmerHMM_glimmerT_31529-T1
Valid prediction for GeneMark_model.54336_t
Valid prediction for GlimmerHMM_glimmerT_31516-T1
Valid prediction for GeneMark_model.54326_t
Valid prediction for GlimmerHMM_glimmerT_31539-T1
Valid prediction for Augustus_model.g21051.t1
Valid prediction for Augustus_model.g21049.t1
Valid prediction for GlimmerHMM_glimmerT_31527-T1
Valid prediction for GlimmerHMM_glimmerT_31535-T1
Valid prediction for GeneMark_model.54322_t
Valid prediction for GeneMark_model.54323_t
Valid prediction for GeneMark_model.54337_t
Valid prediction for GeneMark_model.54327_t
Valid prediction for GlimmerHMM_glimmerT_31534-T1
Valid prediction for GeneMark_model.54320_t
Valid prediction for GlimmerHMM_glimmerT_31542-T1
Valid prediction for GeneMark_model.54334_t
Valid prediction for GlimmerHMM_glimmerT_31523-T1
Valid prediction for snap_scaffold_12-snap.3231-T1
Valid prediction for Augustus_model.g21064.t1
Valid prediction for GlimmerHMM_glimmerT_31541-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_12-snap.3242-T1
Valid prediction for CodingQuarry_transcript_10502-T1
Valid prediction for GlimmerHMM_glimmerT_31528-T1
Valid prediction for GlimmerHMM_glimmerT_31533-T1
Valid prediction for GeneMark_model.54321_t
Valid prediction for Augustus_model.g21057.t1
Valid prediction for GlimmerHMM_glimmerT_31530-T1
Valid prediction for Augustus_model.g21059.t1
Valid prediction for snap_scaffold_12-snap.3247-T1
Valid prediction for GlimmerHMM_glimmerT_31540-T1
Valid prediction for snap_scaffold_12-snap.3243-T1
Valid prediction for GeneMark_model.54329_t
Valid prediction for snap_scaffold_12-snap.3226-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g21067.t1
Valid prediction for Augustus_model.g21068.t1
Valid prediction for HiQ_model.g21058.t1
Valid prediction for pasa_asmbl_8281.p1
Valid prediction for GeneMark_model.54342_t
Valid prediction for GeneMark_model.54319_t
Valid prediction for GlimmerHMM_glimmerT_31519-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.3244-T1
Valid prediction for GeneMark_model.54340_t
Valid prediction for Augustus_model.g21056.t1
Valid prediction for snap_scaffold_12-snap.3246-T1
Valid prediction for snap_scaffold_12-snap.3232-T1
Valid prediction for Augustus_model.g21055.t1
Valid prediction for GeneMark_model.54339_t
Valid prediction for Augustus_model.g21066.t1
Valid prediction for snap_scaffold_12-snap.3236-T1
Valid prediction for Augustus_model.g21047.t1
Valid prediction for Augustus_model.g21053.t1
Valid prediction for GlimmerHMM_glimmerT_31517-T1
Valid prediction for GeneMark_model.54345_t
Valid prediction for GeneMark_model.54341_t
Valid prediction for snap_scaffold_12-snap.3245-T1
Valid prediction for snap_scaffold_12-snap.3238-T1
Valid prediction for GlimmerHMM_glimmerT_31538-T1
Valid prediction for GlimmerHMM_glimmerT_31525-T1
Valid prediction for GlimmerHMM_glimmerT_31536-T1
Valid prediction for Augustus_model.g21063.t1
Valid prediction for GlimmerHMM_glimmerT_31532-T1
Valid prediction for Augustus_model.g21065.t1
Valid prediction for snap_scaffold_12-snap.3239-T1
Valid prediction for snap_scaffold_12-snap.3235-T1
Valid prediction for GlimmerHMM_glimmerT_31526-T1

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

-building trellis in range 1 - 178297
-exon list size: 268


building trellis

0.4    
0.7    
1.1    
1.5    
1.9    
2.2    
2.6    
3.0    
3.3    
3.7    
4.1    
4.4    
4.8    
5.2    
5.6    
5.9    
6.3    
6.7    
7.0    
7.4    
7.8    
8.1    
8.5    
8.9    
9.3    
9.6    
10.0    
10.4    
10.7    
11.1    
11.5    
11.9    
12.2    
12.6    
13.0    
13.3    
13.7    
14.1    
14.4    
14.8    
15.2    
15.6    
15.9    
16.3    
16.7    
17.0    
17.4    
17.8    
18.1    
18.5    
18.9    
19.3    
19.6    
20.0    
20.4    
20.7    
21.1    
21.5    
21.9    
22.2    
22.6    
23.0    
23.3    
23.7    
24.1    
24.4    
24.8    
25.2    
25.6    
25.9    
26.3    
26.7    
27.0    
27.4    
27.8    
28.1    
28.5    
28.9    
29.3    
29.6    
30.0    
30.4    
30.7    
31.1    
31.5    
31.9    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.4    
34.8    
35.2    
35.6    
35.9    
36.3    
36.7    
37.0    
37.4    
37.8    
38.1    
38.5    
38.9    
39.3    
39.6    
40.0    
40.4    
40.7    
41.1    
41.5    
41.9    
42.2    
42.6    
43.0    
43.3    
43.7    
44.1    
44.4    
44.8    
45.2    
45.6    
45.9    
46.3    
46.7    
47.0    
47.4    
47.8    
48.1    
48.5    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.5    
51.9    
52.2    
52.6    
53.0    
53.3    
53.7    
54.1    
54.4    
54.8    
55.2    
55.6    
55.9    
56.3    
56.7    
57.0    
57.4    
57.8    
58.1    
58.5    
58.9    
59.3    
59.6    
60.0    
60.4    
60.7    
61.1    
61.5    
61.9    
62.2    
62.6    
63.0    
63.3    
63.7    
64.1    
64.4    
64.8    
65.2    
65.6    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.1    
68.5    
68.9    
69.3    
69.6    
70.0    
70.4    
70.7    
71.1    
71.5    
71.9    
72.2    
72.6    
73.0    
73.3    
73.7    
74.1    
74.4    
74.8    
75.2    
75.6    
75.9    
76.3    
76.7    
77.0    
77.4    
77.8    
78.1    
78.5    
78.9    
79.3    
79.6    
80.0    
80.4    
80.7    
81.1    
81.5    
81.9    
82.2    
82.6    
83.0    
83.3    
83.7    
84.1    
84.4    
84.8    
85.2    
85.6    
85.9    
86.3    
86.7    
87.0    
87.4    
87.8    
88.1    
88.5    
88.9    
89.3    
89.6    
90.0    
90.4    
90.7    
91.1    
91.5    
91.9    
92.2    
92.6    
93.0    
93.3    
93.7    
94.1    
94.4    
94.8    
95.2    
95.6    
95.9    
96.3    
96.7    
97.0    
97.4    
97.8    
98.1    
98.5    
98.9    
99.3    
99.6    
-found 27 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 26814
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-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 - 26338
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-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

-building DP trellis

-building trellis in range 1 - 24367
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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 9268 - 24367
-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 9632 - 24367
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 10264 - 24367
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 11348 - 24367
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 11348 - 23271
-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