-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_380155-645255

-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 snap_scaffold_4-snap.95-T1
Valid prediction for GlimmerHMM_glimmerT_8641-T1
Valid prediction for snap_scaffold_4-snap.132-T1
Valid prediction for GlimmerHMM_glimmerT_8645-T1
Valid prediction for snap_scaffold_4-snap.99-T1
Valid prediction for snap_scaffold_4-snap.119-T1
Valid prediction for snap_scaffold_4-snap.91-T1
Valid prediction for snap_scaffold_4-snap.87-T1
Valid prediction for snap_scaffold_4-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_8643-T1
Valid prediction for snap_scaffold_4-snap.80-T1
Valid prediction for snap_scaffold_4-snap.114-T1
Valid prediction for GlimmerHMM_glimmerT_8639-T1
Valid prediction for Augustus_model.g5611.t1
Valid prediction for snap_scaffold_4-snap.128-T1
Valid prediction for GlimmerHMM_glimmerT_8629-T1
Valid prediction for snap_scaffold_4-snap.123-T1
Valid prediction for snap_scaffold_4-snap.110-T1
Valid prediction for GlimmerHMM_glimmerT_8636-T1
Valid prediction for GlimmerHMM_glimmerT_8630-T1
Valid prediction for snap_scaffold_4-snap.82-T1
Valid prediction for snap_scaffold_4-snap.125-T1
Valid prediction for snap_scaffold_4-snap.78-T1
Valid prediction for Augustus_model.g5612.t1
Valid prediction for Augustus_model.g5609.t1
Valid prediction for snap_scaffold_4-snap.84-T1
Valid prediction for snap_scaffold_4-snap.100-T1
Valid prediction for snap_scaffold_4-snap.94-T1
Valid prediction for snap_scaffold_4-snap.102-T1
Valid prediction for GlimmerHMM_glimmerT_8642-T1
Valid prediction for GlimmerHMM_glimmerT_8650-T1
Valid prediction for GlimmerHMM_glimmerT_8638-T1
Valid prediction for GlimmerHMM_glimmerT_8631-T1
Valid prediction for snap_scaffold_4-snap.85-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.113-T1
Valid prediction for snap_scaffold_4-snap.118-T1
Valid prediction for snap_scaffold_4-snap.130-T1
Valid prediction for snap_scaffold_4-snap.97-T1
Valid prediction for snap_scaffold_4-snap.106-T1
Valid prediction for snap_scaffold_4-snap.104-T1
Valid prediction for snap_scaffold_4-snap.107-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_4-snap.111-T1
Valid prediction for snap_scaffold_4-snap.112-T1
Valid prediction for GlimmerHMM_glimmerT_8644-T1
Valid prediction for snap_scaffold_4-snap.126-T1
Valid prediction for snap_scaffold_4-snap.86-T1
Valid prediction for snap_scaffold_4-snap.127-T1
Valid prediction for snap_scaffold_4-snap.116-T1
Valid prediction for snap_scaffold_4-snap.79-T1
Valid prediction for snap_scaffold_4-snap.96-T1
Valid prediction for GlimmerHMM_glimmerT_8651-T1
Valid prediction for Augustus_model.g5618.t1
Valid prediction for snap_scaffold_4-snap.98-T1
Valid prediction for Augustus_model.g5616.t1
Valid prediction for GlimmerHMM_glimmerT_8628-T1
Valid prediction for GlimmerHMM_glimmerT_8640-T1
Valid prediction for Augustus_model.g5610.t1
Valid prediction for Augustus_model.g5614.t1
Valid prediction for snap_scaffold_4-snap.93-T1
Valid prediction for GlimmerHMM_glimmerT_8647-T1
Valid prediction for snap_scaffold_4-snap.120-T1
Valid prediction for GlimmerHMM_glimmerT_8634-T1
Couldn't classify 43322, 43436
Sorry, prediction pasa_asmbl_42331.p1 fails validation.
(ATG)	 AA	37073-37255	GT	AGG
(GTG)	 AG	39867-40070	GT	AGG
(GAT)	 AG	41138-41337	GT	AGG
(TTT)	 AG	43322-43436	GT	CTG
-recovered pasa_asmbl_42331.p1, initial, 37073, 37255
-recovered pasa_asmbl_42331.p1, internal, 39867, 40070
-recovered pasa_asmbl_42331.p1, internal, 41138, 41337
-recovered pasa_asmbl_42331.p1, internal, 43322, 43436
Valid prediction for GlimmerHMM_glimmerT_8627-T1
Valid prediction for snap_scaffold_4-snap.129-T1
Couldn't classify 14535, 14667
Sorry, prediction pasa_asmbl_42332.p1 fails validation.
(GAG)	 CA	14535-14667	GT	AGG
(GAG)	 AG	14955-15083	GT	AGG
(AAC)	 AG	15184-15255	GT	CTG
(ATG)	 AG	16114-16124	AC	GAA
-recovered pasa_asmbl_42332.p1, terminal, 16114, 16124
-recovered pasa_asmbl_42332.p1, internal, 14955, 15083
-recovered pasa_asmbl_42332.p1, internal, 15184, 15255
Valid prediction for GlimmerHMM_glimmerT_8646-T1
Valid prediction for GlimmerHMM_glimmerT_8633-T1
Valid prediction for Augustus_model.g5613.t1
Valid prediction for GlimmerHMM_glimmerT_8649-T1
Valid prediction for snap_scaffold_4-snap.108-T1
Valid prediction for snap_scaffold_4-snap.101-T1
Valid prediction for Augustus_model.g5615.t1
Valid prediction for snap_scaffold_4-snap.121-T1
Valid prediction for snap_scaffold_4-snap.103-T1
Valid prediction for snap_scaffold_4-snap.117-T1
Valid prediction for GlimmerHMM_glimmerT_8648-T1
Valid prediction for GlimmerHMM_glimmerT_8654-T1
Valid prediction for snap_scaffold_4-snap.88-T1
Valid prediction for snap_scaffold_4-snap.81-T1
Valid prediction for snap_scaffold_4-snap.122-T1
Valid prediction for snap_scaffold_4-snap.83-T1
Valid prediction for GlimmerHMM_glimmerT_8637-T1
Valid prediction for snap_scaffold_4-snap.89-T1
Valid prediction for snap_scaffold_4-snap.92-T1
Valid prediction for snap_scaffold_4-snap.115-T1
Valid prediction for GlimmerHMM_glimmerT_8652-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8653-T1
Valid prediction for GlimmerHMM_glimmerT_8635-T1
Valid prediction for Augustus_model.g5617.t1
Valid prediction for snap_scaffold_4-snap.131-T1
Valid prediction for snap_scaffold_4-snap.133-T1
Valid prediction for GlimmerHMM_glimmerT_8632-T1
Valid prediction for snap_scaffold_4-snap.105-T1
Valid prediction for snap_scaffold_4-snap.124-T1
Valid prediction for snap_scaffold_4-snap.90-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5805, rend_intergenic: 4220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17249, rend_intergenic: 6335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19424, rend_intergenic: 17760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26494, rend_intergenic: 19843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30776, rend_intergenic: 27307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46509, rend_intergenic: 31615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60593, rend_intergenic: 47294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61893, rend_intergenic: 60660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84182, rend_intergenic: 61924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91460, rend_intergenic: 84236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104051, rend_intergenic: 92078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122260, rend_intergenic: 115969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127727, rend_intergenic: 124248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130190, rend_intergenic: 127771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136309, rend_intergenic: 132300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140713, rend_intergenic: 136761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142431, rend_intergenic: 140977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147330, rend_intergenic: 142674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153315, rend_intergenic: 149674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158315, rend_intergenic: 154394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187066, rend_intergenic: 164552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197724, rend_intergenic: 187334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213936, rend_intergenic: 204936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218459, rend_intergenic: 216483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224338, rend_intergenic: 221435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234883, rend_intergenic: 230352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246428, rend_intergenic: 244366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257038, rend_intergenic: 256394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257747, rend_intergenic: 257099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263461, rend_intergenic: 259950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 265101
-exon list size: 359


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.0    
3.3    
3.6    
3.9    
4.2    
4.4    
4.7    
5.0    
5.3    
5.5    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.5    
7.8    
8.0    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.6    
13.9    
14.1    
14.4    
14.7    
15.0    
15.2    
15.5    
15.8    
16.1    
16.3    
16.6    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.6    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.8    
26.0    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.6    
31.9    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.2    
35.5    
35.7    
36.0    
36.3    
36.6    
36.8    
37.1    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.9    
63.2    
63.4    
63.7    
64.0    
64.3    
64.5    
64.8    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.1    
68.4    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.5    
71.7    
72.0    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
74.0    
74.2    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.2    
76.5    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.4    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.4    
83.7    
83.9    
84.2    
84.5    
84.8    
85.0    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.6    
95.8    
96.1    
96.4    
96.7    
97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 5805, rend_intergenic: 4220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17249, rend_intergenic: 6335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19424, rend_intergenic: 17760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26494, rend_intergenic: 19843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30776, rend_intergenic: 27307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46509, rend_intergenic: 31615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60593, rend_intergenic: 47294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61893, rend_intergenic: 60660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84182, rend_intergenic: 61924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91460, rend_intergenic: 84236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104051, rend_intergenic: 92078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122260, rend_intergenic: 115969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127727, rend_intergenic: 124248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130190, rend_intergenic: 127771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136309, rend_intergenic: 132300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140713, rend_intergenic: 136761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142431, rend_intergenic: 140977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147330, rend_intergenic: 142674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153315, rend_intergenic: 149674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158315, rend_intergenic: 154394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187066, rend_intergenic: 164552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197724, rend_intergenic: 187334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213936, rend_intergenic: 204936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218459, rend_intergenic: 216483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224338, rend_intergenic: 221435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234883, rend_intergenic: 230352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246428, rend_intergenic: 244366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257038, rend_intergenic: 256394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257747, rend_intergenic: 257099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263461, rend_intergenic: 259950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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