-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_15067221-15227393

-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.13024_t
Valid prediction for Augustus_model.g5308.t1
Valid prediction for snap_scaffold_3-snap.2890-T1
Valid prediction for GlimmerHMM_glimmerT_7992-T1
Valid prediction for snap_scaffold_3-snap.2896-T1
Valid prediction for GeneMark_model.13010_t
Couldn't classify 92517, 92618
Couldn't classify 94086, 94252
Sorry, prediction pasa_asmbl_40792.p1 fails validation.
(TTT)	 AG	92517-92618	GT	AGG
(GAC)	 AG	93539-93632	GT	AGG
(GTG)	 AG	94086-94252	GG	CAG
-recovered pasa_asmbl_40792.p1, terminal, 93539, 93632
-recovered pasa_asmbl_40792.p1, internal, 92517, 92618
-recovered pasa_asmbl_40792.p1, internal, 93539, 93632
Valid prediction for snap_scaffold_3-snap.2883-T1
Valid prediction for GlimmerHMM_glimmerT_7994-T1
Valid prediction for GlimmerHMM_glimmerT_8010-T1
Valid prediction for Augustus_model.g5316.t1
Valid prediction for GeneMark_model.13006_t
Valid prediction for GeneMark_model.13034_t
Valid prediction for GeneMark_model.13027_t
Valid prediction for GlimmerHMM_glimmerT_8000-T1
Valid prediction for Augustus_model.g5314.t1
Valid prediction for GeneMark_model.13030_t
Valid prediction for GlimmerHMM_glimmerT_8009-T1
Valid prediction for snap_scaffold_3-snap.2894-T1
Valid prediction for snap_scaffold_3-snap.2893-T1
Valid prediction for Augustus_model.g5315.t1
Valid prediction for GeneMark_model.13000_t
Valid prediction for GeneMark_model.13014_t
Valid prediction for snap_scaffold_3-snap.2880-T1
Valid prediction for snap_scaffold_3-snap.2875-T1
Valid prediction for snap_scaffold_3-snap.2878-T1
Valid prediction for Augustus_model.g5309.t1
Valid prediction for GeneMark_model.13007_t
Valid prediction for GeneMark_model.13020_t
Valid prediction for GeneMark_model.13032_t
Valid prediction for GlimmerHMM_glimmerT_7999-T1
Valid prediction for GeneMark_model.13017_t
Valid prediction for GeneMark_model.13028_t
Valid prediction for GlimmerHMM_glimmerT_8008-T1
Valid prediction for snap_scaffold_3-snap.2898-T1
Valid prediction for Augustus_model.g5317.t1
Valid prediction for GlimmerHMM_glimmerT_8002-T1
Valid prediction for GeneMark_model.13013_t
Valid prediction for snap_scaffold_3-snap.2889-T1
Valid prediction for GlimmerHMM_glimmerT_7991-T1
Valid prediction for Augustus_model.g5321.t1
Valid prediction for Augustus_model.g5322.t1
Valid prediction for snap_scaffold_3-snap.2888-T1
Valid prediction for snap_scaffold_3-snap.2895-T1
Valid prediction for GeneMark_model.13022_t
Valid prediction for snap_scaffold_3-snap.2872-T1
Valid prediction for GlimmerHMM_glimmerT_7989-T1
Valid prediction for snap_scaffold_3-snap.2885-T1
Valid prediction for GlimmerHMM_glimmerT_7998-T1
Valid prediction for Augustus_model.g5312.t1
Valid prediction for GeneMark_model.13002_t
Valid prediction for Augustus_model.g5310.t1
Valid prediction for snap_scaffold_3-snap.2876-T1
Valid prediction for GeneMark_model.13018_t
Valid prediction for GeneMark_model.13004_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.13019_t
Valid prediction for GeneMark_model.13029_t
Valid prediction for GlimmerHMM_glimmerT_7987-T1
Valid prediction for GeneMark_model.13031_t
Valid prediction for Augustus_model.g5318.t1
Valid prediction for Augustus_model.g5307.t1
Valid prediction for Augustus_model.g5323.t1
Valid prediction for GlimmerHMM_glimmerT_8011-T1
Valid prediction for Augustus_model.g5313.t1
Valid prediction for Augustus_model.g5320.t1
Valid prediction for GeneMark_model.13003_t
Valid prediction for snap_scaffold_3-snap.2886-T1
Valid prediction for snap_scaffold_3-snap.2877-T1
Valid prediction for GlimmerHMM_glimmerT_8003-T1
Valid prediction for Augustus_model.g5319.t1
Valid prediction for GeneMark_model.13025_t
Valid prediction for GlimmerHMM_glimmerT_8006-T1
Valid prediction for snap_scaffold_3-snap.2881-T1
Valid prediction for GeneMark_model.13012_t
Valid prediction for GlimmerHMM_glimmerT_8005-T1
Valid prediction for Augustus_model.g5305.t1
Valid prediction for GeneMark_model.13008_t
Valid prediction for GlimmerHMM_glimmerT_7985-T1
Valid prediction for GeneMark_model.13015_t
Valid prediction for GeneMark_model.13026_t
Valid prediction for snap_scaffold_3-snap.2891-T1
Valid prediction for snap_scaffold_3-snap.2873-T1
Valid prediction for GlimmerHMM_glimmerT_8001-T1
Valid prediction for Augustus_model.g5306.t1
Valid prediction for snap_scaffold_3-snap.2870-T1
Valid prediction for GlimmerHMM_glimmerT_7990-T1
Valid prediction for snap_scaffold_3-snap.2874-T1
Valid prediction for snap_scaffold_3-snap.2900-T1
Valid prediction for snap_scaffold_3-snap.2882-T1
Valid prediction for GeneMark_model.13021_t
Valid prediction for GeneMark_model.13005_t
Valid prediction for GlimmerHMM_glimmerT_7997-T1
Valid prediction for GeneMark_model.13009_t
Valid prediction for GlimmerHMM_glimmerT_7986-T1
Valid prediction for GeneMark_model.12999_t
Valid prediction for snap_scaffold_3-snap.2892-T1
Valid prediction for snap_scaffold_3-snap.2887-T1
Valid prediction for GlimmerHMM_glimmerT_7988-T1
Valid prediction for snap_scaffold_3-snap.2899-T1
Valid prediction for snap_scaffold_3-snap.2871-T1
Valid prediction for Augustus_model.g5311.t1
Valid prediction for GlimmerHMM_glimmerT_7996-T1
Valid prediction for GeneMark_model.13016_t
Valid prediction for snap_scaffold_3-snap.2879-T1
Valid prediction for GeneMark_model.13033_t
Valid prediction for snap_scaffold_3-snap.2884-T1
Valid prediction for GlimmerHMM_glimmerT_7995-T1
Valid prediction for GlimmerHMM_glimmerT_8004-T1
Valid prediction for GeneMark_model.13001_t
Valid prediction for GlimmerHMM_glimmerT_7993-T1
Valid prediction for GeneMark_model.13011_t
Valid prediction for snap_scaffold_3-snap.2897-T1
Valid prediction for Augustus_model.g5304.t1
Valid prediction for GlimmerHMM_glimmerT_8007-T1
Valid prediction for GeneMark_model.13023_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 42566, rend_intergenic: 42563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52442, rend_intergenic: 51671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57129, rend_intergenic: 52583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79484, rend_intergenic: 65808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84852, rend_intergenic: 83208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99869, rend_intergenic: 86669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 160173
-exon list size: 427


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
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2.3    
2.6    
2.8    
3.0    
3.3    
3.5    
3.7    
4.0    
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4.9    
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5.6    
5.8    
6.1    
6.3    
6.5    
6.8    
7.0    
7.2    
7.5    
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7.9    
8.2    
8.4    
8.6    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.7    
11.9    
12.1    
12.4    
12.6    
12.8    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
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    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.1    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.3    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
47.3    
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    
52.7    
52.9    
53.1    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.7    
59.0    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.5    
62.7    
62.9    
63.2    
63.4    
63.6    
63.9    
64.1    
64.3    
64.6    
64.8    
65.0    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.2    
70.4    
70.6    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
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    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.4    
91.6    
91.8    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 42566, rend_intergenic: 42563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52442, rend_intergenic: 51671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57129, rend_intergenic: 52583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79484, rend_intergenic: 65808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84852, rend_intergenic: 83208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99869, rend_intergenic: 86669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 147036 - 160173
-exon list size: 42


building trellis

2.3    
4.5    
6.8    
9.1    
11.4    
13.6    
15.9    
18.2    
20.5    
22.7    
25.0    
27.3    
29.5    
31.8    
34.1    
36.4    
38.6    
40.9    
43.2    
45.5    
47.7    
50.0    
52.3    
54.5    
56.8    
59.1    
61.4    
63.6    
65.9    
68.2    
70.5    
72.7    
75.0    
77.3    
79.5    
81.8    
84.1    
86.4    
88.6    
90.9    
93.2    
95.5    
97.7    
-found 1 predictions from path traversal

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