-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_363386-497991

-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 GlimmerHMM_glimmerT_5888-T1
Valid prediction for Augustus_model.g3839.t1
Valid prediction for snap_scaffold_3-snap.110-T1
Valid prediction for GlimmerHMM_glimmerT_5878-T1
Valid prediction for GlimmerHMM_glimmerT_5867-T1
Valid prediction for snap_scaffold_3-snap.104-T1
Valid prediction for GlimmerHMM_glimmerT_5882-T1
Valid prediction for snap_scaffold_3-snap.113-T1
Valid prediction for Augustus_model.g3841.t1
Valid prediction for snap_scaffold_3-snap.92-T1
Valid prediction for snap_scaffold_3-snap.95-T1
Valid prediction for snap_scaffold_3-snap.99-T1
Valid prediction for snap_scaffold_3-snap.108-T1
Valid prediction for snap_scaffold_3-snap.91-T1
Valid prediction for Augustus_model.g3836.t1
Valid prediction for GlimmerHMM_glimmerT_5881-T1
Valid prediction for GlimmerHMM_glimmerT_5874-T1
Valid prediction for snap_scaffold_3-snap.103-T1
Valid prediction for snap_scaffold_3-snap.112-T1
Valid prediction for snap_scaffold_3-snap.90-T1
Valid prediction for snap_scaffold_3-snap.101-T1
Valid prediction for snap_scaffold_3-snap.115-T1
Valid prediction for GlimmerHMM_glimmerT_5870-T1
Valid prediction for snap_scaffold_3-snap.118-T1
Valid prediction for GlimmerHMM_glimmerT_5886-T1
Valid prediction for snap_scaffold_3-snap.93-T1
Valid prediction for GlimmerHMM_glimmerT_5887-T1
Valid prediction for snap_scaffold_3-snap.97-T1
Valid prediction for GlimmerHMM_glimmerT_5880-T1
Valid prediction for snap_scaffold_3-snap.89-T1
Valid prediction for Augustus_model.g3845.t1
Valid prediction for Augustus_model.g3842.t1
Valid prediction for snap_scaffold_3-snap.117-T1
Valid prediction for GlimmerHMM_glimmerT_5883-T1
Valid prediction for snap_scaffold_3-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 Augustus_model.g3840.t1
Valid prediction for snap_scaffold_3-snap.88-T1
Valid prediction for GlimmerHMM_glimmerT_5868-T1
Valid prediction for GlimmerHMM_glimmerT_5876-T1
Valid prediction for snap_scaffold_3-snap.94-T1
Valid prediction for snap_scaffold_3-snap.114-T1
Valid prediction for snap_scaffold_3-snap.116-T1
Valid prediction for snap_scaffold_3-snap.98-T1
Valid prediction for GlimmerHMM_glimmerT_5877-T1
Valid prediction for snap_scaffold_3-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_5872-T1
Valid prediction for Augustus_model.g3837.t1
Valid prediction for Augustus_model.g3835.t1
Valid prediction for GlimmerHMM_glimmerT_5884-T1
Valid prediction for Augustus_model.g3843.t1
Valid prediction for snap_scaffold_3-snap.96-T1
Valid prediction for GlimmerHMM_glimmerT_5869-T1
Valid prediction for GlimmerHMM_glimmerT_5866-T1
Valid prediction for GlimmerHMM_glimmerT_5885-T1
Valid prediction for snap_scaffold_3-snap.111-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.102-T1
Valid prediction for GlimmerHMM_glimmerT_5873-T1
Valid prediction for Augustus_model.g3844.t1
Valid prediction for snap_scaffold_3-snap.100-T1
Valid prediction for GlimmerHMM_glimmerT_5875-T1
Valid prediction for Augustus_model.g3838.t1
Valid prediction for GlimmerHMM_glimmerT_5871-T1
Valid prediction for GlimmerHMM_glimmerT_5879-T1
Valid prediction for snap_scaffold_3-snap.106-T1
Valid prediction for snap_scaffold_3-snap.105-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4563, rend_intergenic: 1988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28432, rend_intergenic: 26433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31569, rend_intergenic: 30705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37426, rend_intergenic: 34125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70647, rend_intergenic: 65574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80136, rend_intergenic: 73557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101751, rend_intergenic: 93406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112177, rend_intergenic: 107462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115284, rend_intergenic: 113664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134606
-exon list size: 197


building trellis

0.5    
1.0    
1.5    
2.0    
2.5    
3.0    
3.5    
4.0    
4.5    
5.0    
5.5    
6.0    
6.5    
7.0    
7.5    
8.0    
8.5    
9.0    
9.5    
10.1    
10.6    
11.1    
11.6    
12.1    
12.6    
13.1    
13.6    
14.1    
14.6    
15.1    
15.6    
16.1    
16.6    
17.1    
17.6    
18.1    
18.6    
19.1    
19.6    
20.1    
20.6    
21.1    
21.6    
22.1    
22.6    
23.1    
23.6    
24.1    
24.6    
25.1    
25.6    
26.1    
26.6    
27.1    
27.6    
28.1    
28.6    
29.1    
29.6    
30.2    
30.7    
31.2    
31.7    
32.2    
32.7    
33.2    
33.7    
34.2    
34.7    
35.2    
35.7    
36.2    
36.7    
37.2    
37.7    
38.2    
38.7    
39.2    
39.7    
40.2    
40.7    
41.2    
41.7    
42.2    
42.7    
43.2    
43.7    
44.2    
44.7    
45.2    
45.7    
46.2    
46.7    
47.2    
47.7    
48.2    
48.7    
49.2    
49.7    
50.3    
50.8    
51.3    
51.8    
52.3    
52.8    
53.3    
53.8    
54.3    
54.8    
55.3    
55.8    
56.3    
56.8    
57.3    
57.8    
58.3    
58.8    
59.3    
59.8    
60.3    
60.8    
61.3    
61.8    
62.3    
62.8    
63.3    
63.8    
64.3    
64.8    
65.3    
65.8    
66.3    
66.8    
67.3    
67.8    
68.3    
68.8    
69.3    
69.8    
70.4    
70.9    
71.4    
71.9    
72.4    
72.9    
73.4    
73.9    
74.4    
74.9    
75.4    
75.9    
76.4    
76.9    
77.4    
77.9    
78.4    
78.9    
79.4    
79.9    
80.4    
80.9    
81.4    
81.9    
82.4    
82.9    
83.4    
83.9    
84.4    
84.9    
85.4    
85.9    
86.4    
86.9    
87.4    
87.9    
88.4    
88.9    
89.4    
89.9    
90.5    
91.0    
91.5    
92.0    
92.5    
93.0    
93.5    
94.0    
94.5    
95.0    
95.5    
96.0    
96.5    
97.0    
97.5    
98.0    
98.5    
99.0    
99.5    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 4563, rend_intergenic: 1988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28432, rend_intergenic: 26433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31569, rend_intergenic: 30705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37426, rend_intergenic: 34125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70647, rend_intergenic: 65574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80136, rend_intergenic: 73557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101751, rend_intergenic: 93406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112177, rend_intergenic: 107462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115284, rend_intergenic: 113664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support