-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_12452542-12580460

-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_2-snap.2372-T1
Valid prediction for Augustus_model.g3116.t1
Valid prediction for Augustus_model.g3123.t1
Valid prediction for GlimmerHMM_glimmerT_4653-T1
Valid prediction for GlimmerHMM_glimmerT_4640-T1
Valid prediction for GlimmerHMM_glimmerT_4637-T1
Valid prediction for Augustus_model.g3121.t1
Valid prediction for GlimmerHMM_glimmerT_4651-T1
Valid prediction for GlimmerHMM_glimmerT_4647-T1
Valid prediction for snap_scaffold_2-snap.2387-T1
Valid prediction for Augustus_model.g3130.t1
Valid prediction for GlimmerHMM_glimmerT_4638-T1
Valid prediction for Augustus_model.g3128.t1
Valid prediction for Augustus_model.g3119.t1
Valid prediction for GlimmerHMM_glimmerT_4657-T1
Valid prediction for snap_scaffold_2-snap.2365-T1
Valid prediction for GlimmerHMM_glimmerT_4652-T1
Valid prediction for GlimmerHMM_glimmerT_4642-T1
Valid prediction for snap_scaffold_2-snap.2358-T1
Valid prediction for snap_scaffold_2-snap.2377-T1
Valid prediction for snap_scaffold_2-snap.2367-T1
Valid prediction for snap_scaffold_2-snap.2359-T1
Valid prediction for snap_scaffold_2-snap.2385-T1
Valid prediction for snap_scaffold_2-snap.2383-T1
Valid prediction for snap_scaffold_2-snap.2375-T1
Couldn't classify 63479, 63796
Sorry, prediction pasa_asmbl_24797.p1 fails validation.
(GAA)	 CA	63479-63796	CC	GAC
Valid prediction for snap_scaffold_2-snap.2370-T1
Valid prediction for snap_scaffold_2-snap.2363-T1
Valid prediction for snap_scaffold_2-snap.2384-T1
Valid prediction for snap_scaffold_2-snap.2357-T1
Valid prediction for snap_scaffold_2-snap.2356-T1
Valid prediction for CodingQuarry_transcript_28682-T1
Valid prediction for GlimmerHMM_glimmerT_4654-T1
Valid prediction for GlimmerHMM_glimmerT_4650-T1
Valid prediction for snap_scaffold_2-snap.2388-T1
Valid prediction for Augustus_model.g3131.t1
Valid prediction for Augustus_model.g3129.t1
Valid prediction for snap_scaffold_2-snap.2381-T1
Valid prediction for Augustus_model.g3118.t1
Valid prediction for snap_scaffold_2-snap.2380-T1
Valid prediction for Augustus_model.g3117.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_2-snap.2366-T1
Valid prediction for Augustus_model.g3125.t1
Valid prediction for GlimmerHMM_glimmerT_4639-T1
Valid prediction for GlimmerHMM_glimmerT_4655-T1
Couldn't classify 88228, 88530
Sorry, prediction pasa_asmbl_24796.p1 fails validation.
(CAT)	 AC	88228-88530	GG	GAG
Valid prediction for snap_scaffold_2-snap.2360-T1
Valid prediction for Augustus_model.g3120.t1
Valid prediction for GlimmerHMM_glimmerT_4636-T1
Valid prediction for snap_scaffold_2-snap.2373-T1
Valid prediction for snap_scaffold_2-snap.2374-T1
Valid prediction for GlimmerHMM_glimmerT_4645-T1
Valid prediction for Augustus_model.g3122.t1
Valid prediction for GlimmerHMM_glimmerT_4649-T1
Valid prediction for snap_scaffold_2-snap.2369-T1
Valid prediction for snap_scaffold_2-snap.2379-T1
Valid prediction for Augustus_model.g3127.t1
Valid prediction for snap_scaffold_2-snap.2382-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.2386-T1
Valid prediction for snap_scaffold_2-snap.2355-T1
Valid prediction for Augustus_model.g3126.t1
Valid prediction for GlimmerHMM_glimmerT_4656-T1
Valid prediction for GlimmerHMM_glimmerT_4643-T1
Valid prediction for snap_scaffold_2-snap.2362-T1
Valid prediction for snap_scaffold_2-snap.2376-T1
Valid prediction for GlimmerHMM_glimmerT_4648-T1
Valid prediction for GlimmerHMM_glimmerT_4646-T1
Valid prediction for GlimmerHMM_glimmerT_4641-T1
Valid prediction for Augustus_model.g3124.t1
Valid prediction for snap_scaffold_2-snap.2364-T1
Valid prediction for GlimmerHMM_glimmerT_4644-T1
Valid prediction for snap_scaffold_2-snap.2368-T1
Valid prediction for snap_scaffold_2-snap.2378-T1
Valid prediction for snap_scaffold_2-snap.2361-T1
Valid prediction for snap_scaffold_2-snap.2371-T1
Valid prediction for snap_scaffold_2-snap.2389-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7920, rend_intergenic: 3598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25044, rend_intergenic: 15721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27569, rend_intergenic: 25676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32221, rend_intergenic: 29184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38656, rend_intergenic: 34661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50920, rend_intergenic: 42829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54494, rend_intergenic: 51659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55532, rend_intergenic: 54827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58087, rend_intergenic: 56051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64015, rend_intergenic: 58873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69475, rend_intergenic: 66389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77003, rend_intergenic: 73850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92029, rend_intergenic: 84978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94342, rend_intergenic: 94289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100247, rend_intergenic: 94460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115658, rend_intergenic: 112756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126088, rend_intergenic: 118243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 127919
-exon list size: 259


building trellis

0.4    
0.8    
1.1    
1.5    
1.9    
2.3    
2.7    
3.1    
3.4    
3.8    
4.2    
4.6    
5.0    
5.4    
5.7    
6.1    
6.5    
6.9    
7.3    
7.7    
8.0    
8.4    
8.8    
9.2    
9.6    
10.0    
10.3    
10.7    
11.1    
11.5    
11.9    
12.3    
12.6    
13.0    
13.4    
13.8    
14.2    
14.6    
14.9    
15.3    
15.7    
16.1    
16.5    
16.9    
17.2    
17.6    
18.0    
18.4    
18.8    
19.2    
19.5    
19.9    
20.3    
20.7    
21.1    
21.5    
21.8    
22.2    
22.6    
23.0    
23.4    
23.8    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.4    
26.8    
27.2    
27.6    
28.0    
28.4    
28.7    
29.1    
29.5    
29.9    
30.3    
30.7    
31.0    
31.4    
31.8    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.5    
34.9    
35.2    
35.6    
36.0    
36.4    
36.8    
37.2    
37.5    
37.9    
38.3    
38.7    
39.1    
39.5    
39.8    
40.2    
40.6    
41.0    
41.4    
41.8    
42.1    
42.5    
42.9    
43.3    
43.7    
44.1    
44.4    
44.8    
45.2    
45.6    
46.0    
46.4    
46.7    
47.1    
47.5    
47.9    
48.3    
48.7    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.3    
51.7    
52.1    
52.5    
52.9    
53.3    
53.6    
54.0    
54.4    
54.8    
55.2    
55.6    
55.9    
56.3    
56.7    
57.1    
57.5    
57.9    
58.2    
58.6    
59.0    
59.4    
59.8    
60.2    
60.5    
60.9    
61.3    
61.7    
62.1    
62.5    
62.8    
63.2    
63.6    
64.0    
64.4    
64.8    
65.1    
65.5    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.2    
68.6    
69.0    
69.3    
69.7    
70.1    
70.5    
70.9    
71.3    
71.6    
72.0    
72.4    
72.8    
73.2    
73.6    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.2    
76.6    
77.0    
77.4    
77.8    
78.2    
78.5    
78.9    
79.3    
79.7    
80.1    
80.5    
80.8    
81.2    
81.6    
82.0    
82.4    
82.8    
83.1    
83.5    
83.9    
84.3    
84.7    
85.1    
85.4    
85.8    
86.2    
86.6    
87.0    
87.4    
87.7    
88.1    
88.5    
88.9    
89.3    
89.7    
90.0    
90.4    
90.8    
91.2    
91.6    
92.0    
92.3    
92.7    
93.1    
93.5    
93.9    
94.3    
94.6    
95.0    
95.4    
95.8    
96.2    
96.6    
96.9    
97.3    
97.7    
98.1    
98.5    
98.9    
99.2    
99.6    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 7920, rend_intergenic: 3598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25044, rend_intergenic: 15721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27569, rend_intergenic: 25676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32221, rend_intergenic: 29184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38656, rend_intergenic: 34661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50920, rend_intergenic: 42829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54494, rend_intergenic: 51659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55532, rend_intergenic: 54827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58087, rend_intergenic: 56051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64015, rend_intergenic: 58873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69475, rend_intergenic: 66389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77003, rend_intergenic: 73850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92029, rend_intergenic: 84978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94342, rend_intergenic: 94289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100247, rend_intergenic: 94460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115658, rend_intergenic: 112756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126088, rend_intergenic: 118243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support