-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_18448749-18624110

-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_1-snap.3391-T1
Valid prediction for GlimmerHMM_glimmerT_2476-T1
Valid prediction for snap_scaffold_1-snap.3403-T1
Valid prediction for GlimmerHMM_glimmerT_2492-T1
Valid prediction for Augustus_model.g1806.t1
Valid prediction for snap_scaffold_1-snap.3375-T1
Valid prediction for GlimmerHMM_glimmerT_2470-T1
Valid prediction for snap_scaffold_1-snap.3410-T1
Valid prediction for snap_scaffold_1-snap.3384-T1
Valid prediction for Augustus_model.g1805.t1
Valid prediction for GlimmerHMM_glimmerT_2474-T1
Valid prediction for snap_scaffold_1-snap.3365-T1
Valid prediction for snap_scaffold_1-snap.3392-T1
Valid prediction for snap_scaffold_1-snap.3408-T1
Valid prediction for GlimmerHMM_glimmerT_2487-T1
Valid prediction for snap_scaffold_1-snap.3400-T1
Valid prediction for snap_scaffold_1-snap.3401-T1
Valid prediction for GlimmerHMM_glimmerT_2477-T1
Valid prediction for GlimmerHMM_glimmerT_2488-T1
Valid prediction for GlimmerHMM_glimmerT_2485-T1
Valid prediction for Augustus_model.g1810.t1
Valid prediction for GlimmerHMM_glimmerT_2473-T1
Valid prediction for snap_scaffold_1-snap.3389-T1
Valid prediction for Augustus_model.g1804.t1
Valid prediction for snap_scaffold_1-snap.3407-T1
Valid prediction for snap_scaffold_1-snap.3395-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2471-T1
Valid prediction for GlimmerHMM_glimmerT_2491-T1
Valid prediction for Augustus_model.g1817.t1
Valid prediction for snap_scaffold_1-snap.3398-T1
Valid prediction for snap_scaffold_1-snap.3405-T1
Valid prediction for GlimmerHMM_glimmerT_2494-T1
Valid prediction for snap_scaffold_1-snap.3378-T1
Valid prediction for snap_scaffold_1-snap.3387-T1
Valid prediction for Augustus_model.g1809.t1
Valid prediction for snap_scaffold_1-snap.3372-T1
Valid prediction for Augustus_model.g1816.t1
Valid prediction for snap_scaffold_1-snap.3377-T1
Valid prediction for snap_scaffold_1-snap.3396-T1
Valid prediction for snap_scaffold_1-snap.3370-T1
Valid prediction for snap_scaffold_1-snap.3380-T1
Valid prediction for snap_scaffold_1-snap.3368-T1
Valid prediction for Augustus_model.g1815.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_1-snap.3369-T1
Valid prediction for GlimmerHMM_glimmerT_2483-T1
Valid prediction for Augustus_model.g1819.t1
Valid prediction for GlimmerHMM_glimmerT_2490-T1
Valid prediction for snap_scaffold_1-snap.3374-T1
Valid prediction for snap_scaffold_1-snap.3381-T1
Valid prediction for snap_scaffold_1-snap.3367-T1
Valid prediction for GlimmerHMM_glimmerT_2489-T1
Valid prediction for GlimmerHMM_glimmerT_2484-T1
Valid prediction for GlimmerHMM_glimmerT_2478-T1
Valid prediction for Augustus_model.g1803.t1
Valid prediction for snap_scaffold_1-snap.3379-T1
Valid prediction for Augustus_model.g1814.t1
Valid prediction for snap_scaffold_1-snap.3385-T1
Valid prediction for GlimmerHMM_glimmerT_2493-T1
Valid prediction for HiQ_model.g1807.t1
Valid prediction for snap_scaffold_1-snap.3390-T1
Valid prediction for snap_scaffold_1-snap.3397-T1
Valid prediction for Augustus_model.g1818.t1
Valid prediction for GlimmerHMM_glimmerT_2486-T1
Valid prediction for GlimmerHMM_glimmerT_2475-T1
Valid prediction for snap_scaffold_1-snap.3373-T1
Couldn't classify 107585, 107729
Sorry, prediction pasa_asmbl_1118.p1 fails validation.
(GGT)	 TA	107585-107729	GT	AGG
(GTC)	 AG	107944-108723	GT	GGG
(GAC)	 AG	108865-109109	CG	AAC
-recovered pasa_asmbl_1118.p1, terminal, 108865, 109109
-recovered pasa_asmbl_1118.p1, internal, 107944, 108723
Valid prediction for Augustus_model.g1813.t1
Valid prediction for GlimmerHMM_glimmerT_2479-T1
Valid prediction for snap_scaffold_1-snap.3406-T1
Valid prediction for snap_scaffold_1-snap.3404-T1
Valid prediction for GlimmerHMM_glimmerT_2482-T1
Valid prediction for GlimmerHMM_glimmerT_2469-T1
Valid prediction for snap_scaffold_1-snap.3382-T1
Valid prediction for snap_scaffold_1-snap.3402-T1
Valid prediction for GlimmerHMM_glimmerT_2472-T1
Valid prediction for snap_scaffold_1-snap.3371-T1
Valid prediction for snap_scaffold_1-snap.3409-T1
Valid prediction for GlimmerHMM_glimmerT_2480-T1
Valid prediction for snap_scaffold_1-snap.3366-T1
Valid prediction for snap_scaffold_1-snap.3376-T1
Valid prediction for GlimmerHMM_glimmerT_2481-T1
Valid prediction for Augustus_model.g1811.t1
Valid prediction for snap_scaffold_1-snap.3399-T1
Valid prediction for Augustus_model.g1808.t1
Valid prediction for snap_scaffold_1-snap.3394-T1
Valid prediction for snap_scaffold_1-snap.3393-T1
Valid prediction for snap_scaffold_1-snap.3388-T1
Valid prediction for snap_scaffold_1-snap.3386-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for pasa_asmbl_1107.p1
Valid prediction for snap_scaffold_1-snap.3383-T1
Valid prediction for CodingQuarry_transcript_3001-T1
Valid prediction for Augustus_model.g1812.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16162, rend_intergenic: 13914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17608, rend_intergenic: 16609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20138, rend_intergenic: 17754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30135, rend_intergenic: 25300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53780, rend_intergenic: 48967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62911, rend_intergenic: 58399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97824, rend_intergenic: 92175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103257, rend_intergenic: 98984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111643, rend_intergenic: 108196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128870, rend_intergenic: 127079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132237, rend_intergenic: 129671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135365, rend_intergenic: 132553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135663, rend_intergenic: 135570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148847, rend_intergenic: 136290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152637, rend_intergenic: 149513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153325, rend_intergenic: 152796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156792, rend_intergenic: 153754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162052, rend_intergenic: 158928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170364, rend_intergenic: 167368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173939, rend_intergenic: 170657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175362
-exon list size: 341


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 16162, rend_intergenic: 13914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17608, rend_intergenic: 16609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20138, rend_intergenic: 17754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30135, rend_intergenic: 25300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53780, rend_intergenic: 48967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62911, rend_intergenic: 58399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97824, rend_intergenic: 92175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103257, rend_intergenic: 98984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111643, rend_intergenic: 108196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128870, rend_intergenic: 127079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132237, rend_intergenic: 129671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135365, rend_intergenic: 132553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135663, rend_intergenic: 135570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148847, rend_intergenic: 136290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152637, rend_intergenic: 149513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153325, rend_intergenic: 152796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156792, rend_intergenic: 153754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162052, rend_intergenic: 158928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170364, rend_intergenic: 167368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173939, rend_intergenic: 170657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support