-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_4972514-5132385

-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.67008_t
Valid prediction for snap_scaffold_16-snap.986-T1
Valid prediction for snap_scaffold_16-snap.988-T1
Valid prediction for snap_scaffold_16-snap.996-T1
Valid prediction for GeneMark_model.67007_t
Valid prediction for GeneMark_model.67037_t
Valid prediction for snap_scaffold_16-snap.977-T1
Valid prediction for GeneMark_model.67012_t
Valid prediction for GlimmerHMM_glimmerT_39141-T1
Valid prediction for snap_scaffold_16-snap.975-T1
Valid prediction for GlimmerHMM_glimmerT_39135-T1
Valid prediction for GeneMark_model.67004_t
Valid prediction for GeneMark_model.66996_t
Valid prediction for GeneMark_model.67035_t
Valid prediction for snap_scaffold_16-snap.979-T1
Valid prediction for GlimmerHMM_glimmerT_39134-T1
Valid prediction for snap_scaffold_16-snap.990-T1
Valid prediction for GeneMark_model.67039_t
Valid prediction for Augustus_model.g26288.t1
Valid prediction for GeneMark_model.67011_t
Valid prediction for GeneMark_model.67014_t
Valid prediction for snap_scaffold_16-snap.962-T1
Valid prediction for Augustus_model.g26286.t1
Valid prediction for GeneMark_model.67020_t
Valid prediction for GeneMark_model.67032_t
Valid prediction for Augustus_model.g26287.t1
Valid prediction for snap_scaffold_16-snap.964-T1
Couldn't classify 45435, 45643
Couldn't classify 46742, 46889
Sorry, prediction pasa_asmbl_17544.p1 fails validation.
(GGC)	 CA	45435-45643	GT	AAG
(ACT)	 AG	46742-46889	GT	AGG
-recovered pasa_asmbl_17544.p1, internal, 46742, 46889
Valid prediction for snap_scaffold_16-snap.991-T1
Valid prediction for snap_scaffold_16-snap.987-T1
Valid prediction for GeneMark_model.67017_t
Valid prediction for GeneMark_model.67027_t
Valid prediction for snap_scaffold_16-snap.981-T1
Valid prediction for GeneMark_model.66998_t
Valid prediction for snap_scaffold_16-snap.994-T1
Couldn't classify 50595, 50636
Couldn't classify 54336, 54386
Sorry, prediction pasa_asmbl_17565.p1 fails validation.
(GCT)	 GT	50595-50636	GT	AGG
(CCA)	 AG	52451-52633	GT	AGG
(GTG)	 AG	53919-54095	GT	AGG
(TTT)	 AG	54336-54386	CG	ACC
-recovered pasa_asmbl_17565.p1, internal, 52451, 52633
-recovered pasa_asmbl_17565.p1, internal, 53919, 54095
Valid prediction for Augustus_model.g26292.t1
Valid prediction for snap_scaffold_16-snap.959-T1
Valid prediction for GeneMark_model.67018_t
Valid prediction for GeneMark_model.66994_t
Valid prediction for GeneMark_model.67002_t
Valid prediction for GeneMark_model.67024_t
Valid prediction for snap_scaffold_16-snap.968-T1
Valid prediction for snap_scaffold_16-snap.985-T1
Valid prediction for snap_scaffold_16-snap.983-T1
Valid prediction for snap_scaffold_16-snap.958-T1
Valid prediction for snap_scaffold_16-snap.993-T1
Valid prediction for GlimmerHMM_glimmerT_39142-T1
Valid prediction for GeneMark_model.67030_t
Valid prediction for snap_scaffold_16-snap.980-T1
Valid prediction for snap_scaffold_16-snap.972-T1
Valid prediction for GeneMark_model.67016_t
Valid prediction for GlimmerHMM_glimmerT_39138-T1
Valid prediction for GeneMark_model.67023_t

-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 GeneMark_model.67019_t
Valid prediction for snap_scaffold_16-snap.982-T1
Valid prediction for GlimmerHMM_glimmerT_39132-T1
Valid prediction for GeneMark_model.67022_t
Valid prediction for GeneMark_model.67015_t
Valid prediction for GlimmerHMM_glimmerT_39133-T1
Valid prediction for GeneMark_model.67026_t
Valid prediction for snap_scaffold_16-snap.995-T1
Valid prediction for GlimmerHMM_glimmerT_39143-T1
Valid prediction for GlimmerHMM_glimmerT_39140-T1
Valid prediction for GlimmerHMM_glimmerT_39144-T1
Couldn't classify 80566, 80636
Sorry, prediction pasa_asmbl_16259.p1 fails validation.
(GAT)	 CT	80566-80636	GT	CAG
(GGA)	 AG	80779-81142	GG	GAG
-recovered pasa_asmbl_16259.p1, terminal, 80779, 81142
Valid prediction for GeneMark_model.66995_t
Valid prediction for GlimmerHMM_glimmerT_39146-T1
Valid prediction for Augustus_model.g26298.t1
Valid prediction for GeneMark_model.67005_t
Valid prediction for snap_scaffold_16-snap.984-T1
Valid prediction for GeneMark_model.67031_t
Valid prediction for snap_scaffold_16-snap.992-T1
Valid prediction for Augustus_model.g26289.t1
Valid prediction for snap_scaffold_16-snap.969-T1
Valid prediction for snap_scaffold_16-snap.978-T1
Valid prediction for GeneMark_model.67006_t
Valid prediction for GeneMark_model.67010_t
Valid prediction for GlimmerHMM_glimmerT_39145-T1
Valid prediction for GeneMark_model.66999_t
Valid prediction for GeneMark_model.67034_t
Valid prediction for GeneMark_model.67033_t
Valid prediction for GlimmerHMM_glimmerT_39139-T1
Valid prediction for Augustus_model.g26295.t1
Valid prediction for snap_scaffold_16-snap.989-T1
Valid prediction for Augustus_model.g26285.t1
Valid prediction for snap_scaffold_16-snap.998-T1
Valid prediction for GlimmerHMM_glimmerT_39137-T1
Valid prediction for snap_scaffold_16-snap.973-T1
Valid prediction for GeneMark_model.67029_t
Valid prediction for GeneMark_model.67025_t
Valid prediction for snap_scaffold_16-snap.965-T1
Valid prediction for Augustus_model.g26291.t1
Valid prediction for GlimmerHMM_glimmerT_39136-T1
Valid prediction for Augustus_model.g26296.t1
Valid prediction for GlimmerHMM_glimmerT_39131-T1
Valid prediction for Augustus_model.g26297.t1
Valid prediction for snap_scaffold_16-snap.963-T1
Valid prediction for Augustus_model.g26294.t1
Valid prediction for GlimmerHMM_glimmerT_39148-T1
Valid prediction for snap_scaffold_16-snap.974-T1
Valid prediction for GeneMark_model.67021_t
Valid prediction for snap_scaffold_16-snap.961-T1
Valid prediction for GeneMark_model.67013_t
Valid prediction for GeneMark_model.66997_t
Valid prediction for snap_scaffold_16-snap.960-T1
Valid prediction for GeneMark_model.67000_t
Valid prediction for snap_scaffold_16-snap.976-T1
Valid prediction for snap_scaffold_16-snap.970-T1
Valid prediction for GlimmerHMM_glimmerT_39147-T1
Valid prediction for GeneMark_model.67001_t
Valid prediction for snap_scaffold_16-snap.966-T1
Valid prediction for GeneMark_model.67003_t
Valid prediction for GeneMark_model.67038_t
Valid prediction for Augustus_model.g26290.t1
Valid prediction for snap_scaffold_16-snap.971-T1
Valid prediction for GeneMark_model.67036_t
Valid prediction for snap_scaffold_16-snap.997-T1
Valid prediction for GeneMark_model.67028_t
Valid prediction for snap_scaffold_16-snap.967-T1
Valid prediction for Augustus_model.g26293.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13751, rend_intergenic: 11026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16752, rend_intergenic: 14283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20615, rend_intergenic: 17351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20886, rend_intergenic: 20705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31858, rend_intergenic: 22169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54775, rend_intergenic: 44404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61923, rend_intergenic: 61276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82452, rend_intergenic: 78738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92115, rend_intergenic: 83419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107156, rend_intergenic: 105999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124230, rend_intergenic: 107471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125642, rend_intergenic: 124382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132310, rend_intergenic: 126193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145863, rend_intergenic: 142894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147825, rend_intergenic: 146247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149243, rend_intergenic: 147857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159872
-exon list size: 554


building trellis

0.2    
0.4    
0.5    
0.7    
0.9    
1.1    
1.3    
1.4    
1.6    
1.8    
2.0    
2.2    
2.3    
2.5    
2.7    
2.9    
3.1    
3.2    
3.4    
3.6    
3.8    
4.0    
4.1    
4.3    
4.5    
4.7    
4.9    
5.0    
5.2    
5.4    
5.6    
5.8    
5.9    
6.1    
6.3    
6.5    
6.7    
6.8    
7.0    
7.2    
7.4    
7.6    
7.7    
7.9    
8.1    
8.3    
8.5    
8.6    
8.8    
9.0    
9.2    
9.4    
9.5    
9.7    
9.9    
10.1    
10.3    
10.4    
10.6    
10.8    
11.0    
11.2    
11.3    
11.5    
11.7    
11.9    
12.1    
12.2    
12.4    
12.6    
12.8    
12.9    
13.1    
13.3    
13.5    
13.7    
13.8    
14.0    
14.2    
14.4    
14.6    
14.7    
14.9    
15.1    
15.3    
15.5    
15.6    
15.8    
16.0    
16.2    
16.4    
16.5    
16.7    
16.9    
17.1    
17.3    
17.4    
17.6    
17.8    
18.0    
18.2    
18.3    
18.5    
18.7    
18.9    
19.1    
19.2    
19.4    
19.6    
19.8    
20.0    
20.1    
20.3    
20.5    
20.7    
20.9    
21.0    
21.2    
21.4    
21.6    
21.8    
21.9    
22.1    
22.3    
22.5    
22.7    
22.8    
23.0    
23.2    
23.4    
23.6    
23.7    
23.9    
24.1    
24.3    
24.5    
24.6    
24.8    
25.0    
25.2    
25.4    
25.5    
25.7    
25.9    
26.1    
26.3    
26.4    
26.6    
26.8    
27.0    
27.2    
27.3    
27.5    
27.7    
27.9    
28.1    
28.2    
28.4    
28.6    
28.8    
29.0    
29.1    
29.3    
29.5    
29.7    
29.9    
30.0    
30.2    
30.4    
30.6    
30.8    
30.9    
31.1    
31.3    
31.5    
31.7    
31.8    
32.0    
32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.5    
34.7    
34.9    
35.1    
35.3    
35.4    
35.6    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.5    
38.7    
38.8    
39.0    
39.2    
39.4    
39.6    
39.7    
39.9    
40.1    
40.3    
40.5    
40.6    
40.8    
41.0    
41.2    
41.4    
41.5    
41.7    
41.9    
42.1    
42.3    
42.4    
42.6    
42.8    
43.0    
43.2    
43.3    
43.5    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.8    
45.0    
45.1    
45.3    
45.5    
45.7    
45.9    
46.0    
46.2    
46.4    
46.6    
46.8    
46.9    
47.1    
47.3    
47.5    
47.7    
47.8    
48.0    
48.2    
48.4    
48.6    
48.7    
48.9    
49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
50.5    
50.7    
50.9    
51.1    
51.3    
51.4    
51.6    
51.8    
52.0    
52.2    
52.3    
52.5    
52.7    
52.9    
53.1    
53.2    
53.4    
53.6    
53.8    
54.0    
54.1    
54.3    
54.5    
54.7    
54.9    
55.0    
55.2    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.5    
56.7    
56.8    
57.0    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.1    
60.3    
60.4    
60.6    
60.8    
61.0    
61.2    
61.3    
61.5    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
70.0    
70.1    
70.3    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.6    
71.8    
71.9    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 13751, rend_intergenic: 11026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16752, rend_intergenic: 14283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20615, rend_intergenic: 17351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20886, rend_intergenic: 20705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31858, rend_intergenic: 22169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54775, rend_intergenic: 44404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61923, rend_intergenic: 61276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82452, rend_intergenic: 78738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92115, rend_intergenic: 83419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107156, rend_intergenic: 105999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124230, rend_intergenic: 107471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125642, rend_intergenic: 124382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132310, rend_intergenic: 126193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145863, rend_intergenic: 142894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147825, rend_intergenic: 146247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149243, rend_intergenic: 147857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 137182 - 159872
-exon list size: 54


building trellis

1.8    
3.6    
5.4    
7.1    
8.9    
10.7    
12.5    
14.3    
16.1    
17.9    
19.6    
21.4    
23.2    
25.0    
26.8    
28.6    
30.4    
32.1    
33.9    
35.7    
37.5    
39.3    
41.1    
42.9    
44.6    
46.4    
48.2    
50.0    
51.8    
53.6    
55.4    
57.1    
58.9    
60.7    
62.5    
64.3    
66.1    
67.9    
69.6    
71.4    
73.2    
75.0    
76.8    
78.6    
80.4    
82.1    
83.9    
85.7    
87.5    
89.3    
91.1    
92.9    
94.6    
96.4    
98.2    
-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 137182 - 147887
-exon list size: 35


building trellis

2.7    
5.4    
8.1    
10.8    
13.5    
16.2    
18.9    
21.6    
24.3    
27.0    
29.7    
32.4    
35.1    
37.8    
40.5    
43.2    
45.9    
48.6    
51.4    
54.1    
56.8    
59.5    
62.2    
64.9    
67.6    
70.3    
73.0    
75.7    
78.4    
81.1    
83.8    
86.5    
89.2    
91.9    
94.6    
97.3    
-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 147982 - 159872
-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

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

-building DP trellis

-building trellis in range 148226 - 159872
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-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