-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_18115909-18337659

-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_24350-T1
Valid prediction for GlimmerHMM_glimmerT_24357-T1
Valid prediction for GeneMark_model.41737_t
Valid prediction for GeneMark_model.41735_t
Valid prediction for snap_scaffold_9-snap.3652-T1
Valid prediction for Augustus_model.g16296.t1
Valid prediction for snap_scaffold_9-snap.3668-T1
Valid prediction for snap_scaffold_9-snap.3665-T1
Valid prediction for GlimmerHMM_glimmerT_24352-T1
Valid prediction for snap_scaffold_9-snap.3648-T1
Valid prediction for GeneMark_model.41726_t
Valid prediction for GlimmerHMM_glimmerT_24353-T1
Valid prediction for GeneMark_model.41733_t
Valid prediction for GeneMark_model.41713_t
Valid prediction for GeneMark_model.41732_t
Valid prediction for GlimmerHMM_glimmerT_24351-T1
Valid prediction for GeneMark_model.41706_t
Valid prediction for snap_scaffold_9-snap.3644-T1
Valid prediction for GeneMark_model.41729_t
Valid prediction for GeneMark_model.41723_t
Valid prediction for GeneMark_model.41704_t
Valid prediction for GeneMark_model.41720_t
Valid prediction for Augustus_model.g16298.t1
Valid prediction for snap_scaffold_9-snap.3650-T1
Valid prediction for snap_scaffold_9-snap.3672-T1
Valid prediction for GeneMark_model.41702_t
Valid prediction for snap_scaffold_9-snap.3647-T1
Valid prediction for GeneMark_model.41745_t
Valid prediction for GeneMark_model.41718_t
Valid prediction for Augustus_model.g16294.t1
Valid prediction for GlimmerHMM_glimmerT_24342-T1
Valid prediction for snap_scaffold_9-snap.3661-T1
Valid prediction for GlimmerHMM_glimmerT_24343-T1
Valid prediction for Augustus_model.g16297.t1
Valid prediction for GeneMark_model.41714_t
Valid prediction for GeneMark_model.41700_t
Valid prediction for snap_scaffold_9-snap.3656-T1
Valid prediction for snap_scaffold_9-snap.3667-T1
Valid prediction for snap_scaffold_9-snap.3649-T1
Valid prediction for GeneMark_model.41741_t
Valid prediction for snap_scaffold_9-snap.3658-T1
Valid prediction for snap_scaffold_9-snap.3645-T1
Valid prediction for GlimmerHMM_glimmerT_24348-T1
Valid prediction for GeneMark_model.41709_t
Valid prediction for snap_scaffold_9-snap.3663-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_24360-T1
Valid prediction for GlimmerHMM_glimmerT_24354-T1
Valid prediction for Augustus_model.g16293.t1
Valid prediction for snap_scaffold_9-snap.3657-T1
Valid prediction for GeneMark_model.41717_t
Valid prediction for GeneMark_model.41703_t
Valid prediction for GeneMark_model.41728_t
Valid prediction for snap_scaffold_9-snap.3659-T1
Valid prediction for GlimmerHMM_glimmerT_24355-T1
Valid prediction for GeneMark_model.41724_t
Valid prediction for GeneMark_model.41705_t
Valid prediction for GlimmerHMM_glimmerT_24347-T1
Valid prediction for snap_scaffold_9-snap.3673-T1
Valid prediction for GlimmerHMM_glimmerT_24361-T1
Valid prediction for GeneMark_model.41707_t
Valid prediction for GeneMark_model.41712_t
Valid prediction for GeneMark_model.41739_t
Valid prediction for GeneMark_model.41719_t
Valid prediction for GeneMark_model.41744_t
Valid prediction for GeneMark_model.41740_t
Valid prediction for GeneMark_model.41716_t
Valid prediction for snap_scaffold_9-snap.3655-T1
Valid prediction for GeneMark_model.41743_t
Valid prediction for GeneMark_model.41727_t
Valid prediction for Augustus_model.g16301.t1
Valid prediction for Augustus_model.g16302.t1
Valid prediction for snap_scaffold_9-snap.3671-T1
Valid prediction for GeneMark_model.41725_t
Valid prediction for GlimmerHMM_glimmerT_24349-T1
Valid prediction for GeneMark_model.41734_t
Valid prediction for Augustus_model.g16295.t1
Valid prediction for GeneMark_model.41722_t
Valid prediction for GeneMark_model.41701_t
Valid prediction for GlimmerHMM_glimmerT_24356-T1
Valid prediction for GeneMark_model.41731_t
Valid prediction for snap_scaffold_9-snap.3662-T1
Valid prediction for GeneMark_model.41742_t
Valid prediction for GeneMark_model.41711_t
Valid prediction for GeneMark_model.41738_t
Valid prediction for snap_scaffold_9-snap.3660-T1
Valid prediction for GlimmerHMM_glimmerT_24344-T1
Valid prediction for snap_scaffold_9-snap.3653-T1
Valid prediction for snap_scaffold_9-snap.3646-T1
Valid prediction for GlimmerHMM_glimmerT_24358-T1
Valid prediction for snap_scaffold_9-snap.3670-T1
Valid prediction for snap_scaffold_9-snap.3664-T1
Valid prediction for GeneMark_model.41715_t
Valid prediction for snap_scaffold_9-snap.3643-T1
Valid prediction for GeneMark_model.41708_t
Valid prediction for Augustus_model.g16303.t1
Valid prediction for GeneMark_model.41746_t
Valid prediction for GlimmerHMM_glimmerT_24359-T1
Valid prediction for GeneMark_model.41736_t
Valid prediction for GlimmerHMM_glimmerT_24346-T1
Valid prediction for snap_scaffold_9-snap.3651-T1
Valid prediction for GlimmerHMM_glimmerT_24345-T1
Valid prediction for snap_scaffold_9-snap.3666-T1
Valid prediction for snap_scaffold_9-snap.3654-T1
Valid prediction for Augustus_model.g16300.t1
Valid prediction for GeneMark_model.41710_t
Valid prediction for GeneMark_model.41730_t
Valid prediction for Augustus_model.g16299.t1
Valid prediction for snap_scaffold_9-snap.3669-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26042, rend_intergenic: 5839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32358, rend_intergenic: 27473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66922, rend_intergenic: 64183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79848, rend_intergenic: 77561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106003, rend_intergenic: 104014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180929, rend_intergenic: 172996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188142, rend_intergenic: 183513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202395, rend_intergenic: 188974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218497, rend_intergenic: 210194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 221751
-exon list size: 480


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 26042, rend_intergenic: 5839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32358, rend_intergenic: 27473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66922, rend_intergenic: 64183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79848, rend_intergenic: 77561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106003, rend_intergenic: 104014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180929, rend_intergenic: 172996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188142, rend_intergenic: 183513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202395, rend_intergenic: 188974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218497, rend_intergenic: 210194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 31117
-exon list size: 96


building trellis

1.0    
2.0    
3.1    
4.1    
5.1    
6.1    
7.1    
8.2    
9.2    
10.2    
11.2    
12.2    
13.3    
14.3    
15.3    
16.3    
17.3    
18.4    
19.4    
20.4    
21.4    
22.4    
23.5    
24.5    
25.5    
26.5    
27.6    
28.6    
29.6    
30.6    
31.6    
32.7    
33.7    
34.7    
35.7    
36.7    
37.8    
38.8    
39.8    
40.8    
41.8    
42.9    
43.9    
44.9    
45.9    
46.9    
48.0    
49.0    
50.0    
51.0    
52.0    
53.1    
54.1    
55.1    
56.1    
57.1    
58.2    
59.2    
60.2    
61.2    
62.2    
63.3    
64.3    
65.3    
66.3    
67.3    
68.4    
69.4    
70.4    
71.4    
72.4    
73.5    
74.5    
75.5    
76.5    
77.6    
78.6    
79.6    
80.6    
81.6    
82.7    
83.7    
84.7    
85.7    
86.7    
87.8    
88.8    
89.8    
90.8    
91.8    
92.9    
93.9    
94.9    
95.9    
96.9    
98.0    
99.0    
-found 2 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 - 23420
-exon list size: 73


building trellis

1.3    
2.7    
4.0    
5.3    
6.7    
8.0    
9.3    
10.7    
12.0    
13.3    
14.7    
16.0    
17.3    
18.7    
20.0    
21.3    
22.7    
24.0    
25.3    
26.7    
28.0    
29.3    
30.7    
32.0    
33.3    
34.7    
36.0    
37.3    
38.7    
40.0    
41.3    
42.7    
44.0    
45.3    
46.7    
48.0    
49.3    
50.7    
52.0    
53.3    
54.7    
56.0    
57.3    
58.7    
60.0    
61.3    
62.7    
64.0    
65.3    
66.7    
68.0    
69.3    
70.7    
72.0    
73.3    
74.7    
76.0    
77.3    
78.7    
80.0    
81.3    
82.7    
84.0    
85.3    
86.7    
88.0    
89.3    
90.7    
92.0    
93.3    
94.7    
96.0    
97.3    
98.7    
-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 1 - 21869
-exon list size: 70


building trellis

1.4    
2.8    
4.2    
5.6    
6.9    
8.3    
9.7    
11.1    
12.5    
13.9    
15.3    
16.7    
18.1    
19.4    
20.8    
22.2    
23.6    
25.0    
26.4    
27.8    
29.2    
30.6    
31.9    
33.3    
34.7    
36.1    
37.5    
38.9    
40.3    
41.7    
43.1    
44.4    
45.8    
47.2    
48.6    
50.0    
51.4    
52.8    
54.2    
55.6    
56.9    
58.3    
59.7    
61.1    
62.5    
63.9    
65.3    
66.7    
68.1    
69.4    
70.8    
72.2    
73.6    
75.0    
76.4    
77.8    
79.2    
80.6    
81.9    
83.3    
84.7    
86.1    
87.5    
88.9    
90.3    
91.7    
93.1    
94.4    
95.8    
97.2    
98.6    
-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 - 19920
-exon list size: 65


building trellis

1.5    
3.0    
4.5    
6.0    
7.5    
9.0    
10.4    
11.9    
13.4    
14.9    
16.4    
17.9    
19.4    
20.9    
22.4    
23.9    
25.4    
26.9    
28.4    
29.9    
31.3    
32.8    
34.3    
35.8    
37.3    
38.8    
40.3    
41.8    
43.3    
44.8    
46.3    
47.8    
49.3    
50.7    
52.2    
53.7    
55.2    
56.7    
58.2    
59.7    
61.2    
62.7    
64.2    
65.7    
67.2    
68.7    
70.1    
71.6    
73.1    
74.6    
76.1    
77.6    
79.1    
80.6    
82.1    
83.6    
85.1    
86.6    
88.1    
89.6    
91.0    
92.5    
94.0    
95.5    
97.0    
98.5    
-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 - 17581
-exon list size: 51


building trellis

1.9    
3.8    
5.7    
7.5    
9.4    
11.3    
13.2    
15.1    
17.0    
18.9    
20.8    
22.6    
24.5    
26.4    
28.3    
30.2    
32.1    
34.0    
35.8    
37.7    
39.6    
41.5    
43.4    
45.3    
47.2    
49.1    
50.9    
52.8    
54.7    
56.6    
58.5    
60.4    
62.3    
64.2    
66.0    
67.9    
69.8    
71.7    
73.6    
75.5    
77.4    
79.2    
81.1    
83.0    
84.9    
86.8    
88.7    
90.6    
92.5    
94.3    
96.2    
98.1    
-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 - 13694
-exon list size: 46


building trellis

2.1    
4.2    
6.2    
8.3    
10.4    
12.5    
14.6    
16.7    
18.8    
20.8    
22.9    
25.0    
27.1    
29.2    
31.2    
33.3    
35.4    
37.5    
39.6    
41.7    
43.8    
45.8    
47.9    
50.0    
52.1    
54.2    
56.2    
58.3    
60.4    
62.5    
64.6    
66.7    
68.8    
70.8    
72.9    
75.0    
77.1    
79.2    
81.2    
83.3    
85.4    
87.5    
89.6    
91.7    
93.8    
95.8    
97.9    
-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 1 - 12479
-exon list size: 41


building trellis

2.3    
4.7    
7.0    
9.3    
11.6    
14.0    
16.3    
18.6    
20.9    
23.3    
25.6    
27.9    
30.2    
32.6    
34.9    
37.2    
39.5    
41.9    
44.2    
46.5    
48.8    
51.2    
53.5    
55.8    
58.1    
60.5    
62.8    
65.1    
67.4    
69.8    
72.1    
74.4    
76.7    
79.1    
81.4    
83.7    
86.0    
88.4    
90.7    
93.0    
95.3    
97.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11871
-exon list size: 36


building trellis

2.6    
5.3    
7.9    
10.5    
13.2    
15.8    
18.4    
21.1    
23.7    
26.3    
28.9    
31.6    
34.2    
36.8    
39.5    
42.1    
44.7    
47.4    
50.0    
52.6    
55.3    
57.9    
60.5    
63.2    
65.8    
68.4    
71.1    
73.7    
76.3    
78.9    
81.6    
84.2    
86.8    
89.5    
92.1    
94.7    
97.4    
-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 1 - 11122
-exon list size: 31


building trellis

3.0    
6.1    
9.1    
12.1    
15.2    
18.2    
21.2    
24.2    
27.3    
30.3    
33.3    
36.4    
39.4    
42.4    
45.5    
48.5    
51.5    
54.5    
57.6    
60.6    
63.6    
66.7    
69.7    
72.7    
75.8    
78.8    
81.8    
84.8    
87.9    
90.9    
93.9    
97.0    
-found 1 predictions from path traversal

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