-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_1-205165

-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 Augustus_model.g3816.t1
Valid prediction for snap_scaffold_3-snap.37-T1
Valid prediction for snap_scaffold_3-snap.26-T1
Valid prediction for GlimmerHMM_glimmerT_5833-T1
Valid prediction for GlimmerHMM_glimmerT_5815-T1
Valid prediction for snap_scaffold_3-snap.32-T1
Valid prediction for snap_scaffold_3-snap.18-T1
Valid prediction for snap_scaffold_3-snap.9-T1
Valid prediction for pasa_asmbl_39805.p1
Valid prediction for GlimmerHMM_glimmerT_5817-T1
Valid prediction for GlimmerHMM_glimmerT_5835-T1
Valid prediction for GlimmerHMM_glimmerT_5825-T1
Valid prediction for snap_scaffold_3-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_5840-T1
Valid prediction for GlimmerHMM_glimmerT_5841-T1
Valid prediction for snap_scaffold_3-snap.8-T1
Valid prediction for snap_scaffold_3-snap.38-T1
Valid prediction for Augustus_model.g3820.t1
Valid prediction for GlimmerHMM_glimmerT_5842-T1
Valid prediction for Augustus_model.g3815.t1
Valid prediction for snap_scaffold_3-snap.15-T1
Valid prediction for snap_scaffold_3-snap.19-T1
Valid prediction for snap_scaffold_3-snap.29-T1
Valid prediction for snap_scaffold_3-snap.6-T1
Valid prediction for HiQ_model.g3814.t1
Valid prediction for CodingQuarry_transcript_46062-T1
Valid prediction for GlimmerHMM_glimmerT_5820-T1
Valid prediction for GlimmerHMM_glimmerT_5828-T1
Valid prediction for snap_scaffold_3-snap.14-T1
Valid prediction for GlimmerHMM_glimmerT_5839-T1
Valid prediction for GlimmerHMM_glimmerT_5814-T1
Valid prediction for GlimmerHMM_glimmerT_5837-T1
Valid prediction for snap_scaffold_3-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_5836-T1
Valid prediction for Augustus_model.g3811.t1
Valid prediction for GlimmerHMM_glimmerT_5831-T1
Valid prediction for snap_scaffold_3-snap.12-T1
Valid prediction for GlimmerHMM_glimmerT_5832-T1
Valid prediction for snap_scaffold_3-snap.23-T1
Valid prediction for Augustus_model.g3818.t1
Valid prediction for snap_scaffold_3-snap.20-T1
Valid prediction for snap_scaffold_3-snap.30-T1
Valid prediction for snap_scaffold_3-snap.31-T1
Valid prediction for GlimmerHMM_glimmerT_5822-T1
Valid prediction for snap_scaffold_3-snap.25-T1
Valid prediction for snap_scaffold_3-snap.40-T1
Valid prediction for snap_scaffold_3-snap.24-T1
Valid prediction for snap_scaffold_3-snap.7-T1
Valid prediction for snap_scaffold_3-snap.22-T1
Valid prediction for CodingQuarry_transcript_46061-T1
Valid prediction for snap_scaffold_3-snap.35-T1
Valid prediction for GlimmerHMM_glimmerT_5816-T1
Valid prediction for GlimmerHMM_glimmerT_5818-T1
Valid prediction for GlimmerHMM_glimmerT_5829-T1
Valid prediction for Augustus_model.g3819.t1
Valid prediction for GlimmerHMM_glimmerT_5821-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_3-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_5834-T1
Valid prediction for snap_scaffold_3-snap.17-T1
Valid prediction for snap_scaffold_3-snap.5-T1
Valid prediction for Augustus_model.g3812.t1
Valid prediction for snap_scaffold_3-snap.39-T1
Valid prediction for GlimmerHMM_glimmerT_5838-T1
Valid prediction for Augustus_model.g3817.t1
Valid prediction for snap_scaffold_3-snap.10-T1
Valid prediction for Augustus_model.g3821.t1
Valid prediction for snap_scaffold_3-snap.27-T1
Valid prediction for snap_scaffold_3-snap.34-T1
Valid prediction for GlimmerHMM_glimmerT_5824-T1
Valid prediction for GlimmerHMM_glimmerT_5823-T1
Valid prediction for snap_scaffold_3-snap.21-T1
Valid prediction for GlimmerHMM_glimmerT_5827-T1
Valid prediction for GlimmerHMM_glimmerT_5830-T1
Valid prediction for GlimmerHMM_glimmerT_5819-T1
Valid prediction for snap_scaffold_3-snap.36-T1
Valid prediction for Augustus_model.g3813.t1
Valid prediction for snap_scaffold_3-snap.28-T1
Valid prediction for snap_scaffold_3-snap.41-T1
Valid prediction for snap_scaffold_3-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_5826-T1
Valid prediction for snap_scaffold_3-snap.3-T1
Valid prediction for snap_scaffold_3-snap.13-T1
Valid prediction for snap_scaffold_3-snap.11-T1
Valid prediction for snap_scaffold_3-snap.16-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22807, rend_intergenic: 18160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28932, rend_intergenic: 24060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36754, rend_intergenic: 30423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43595, rend_intergenic: 39095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50892, rend_intergenic: 47190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67830, rend_intergenic: 53040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73967, rend_intergenic: 69467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100309, rend_intergenic: 91897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107518, rend_intergenic: 100342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137388, rend_intergenic: 135783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163478, rend_intergenic: 139510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175037, rend_intergenic: 173135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175790, rend_intergenic: 175750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186716, rend_intergenic: 178887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198852, rend_intergenic: 197768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202157, rend_intergenic: 199405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205165
-exon list size: 313


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.5    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.7    
7.0    
7.3    
7.6    
7.9    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.1    
12.4    
12.7    
13.0    
13.3    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.4    
19.7    
20.0    
20.3    
20.6    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.7    
27.0    
27.3    
27.6    
27.9    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.1    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.4    
39.7    
40.0    
40.3    
40.6    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.7    
47.0    
47.3    
47.6    
47.9    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.1    
52.4    
52.7    
53.0    
53.3    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.4    
59.7    
60.0    
60.3    
60.6    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
67.9    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.1    
72.4    
72.7    
73.0    
73.3    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.4    
79.7    
80.0    
80.3    
80.6    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.7    
87.0    
87.3    
87.6    
87.9    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.1    
92.4    
92.7    
93.0    
93.3    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.5    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 22807, rend_intergenic: 18160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28932, rend_intergenic: 24060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36754, rend_intergenic: 30423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43595, rend_intergenic: 39095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50892, rend_intergenic: 47190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67830, rend_intergenic: 53040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73967, rend_intergenic: 69467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100309, rend_intergenic: 91897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107518, rend_intergenic: 100342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137388, rend_intergenic: 135783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163478, rend_intergenic: 139510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175037, rend_intergenic: 173135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175790, rend_intergenic: 175750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186716, rend_intergenic: 178887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198852, rend_intergenic: 197768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202157, rend_intergenic: 199405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support