-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_363386-496696

-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_6000-T1
Valid prediction for GeneMark_model.9813_t
Valid prediction for Augustus_model.g3949.t1
Valid prediction for snap_scaffold_3-snap.96-T1
Valid prediction for GeneMark_model.9807_t
Valid prediction for GeneMark_model.9794_t
Valid prediction for snap_scaffold_3-snap.92-T1
Valid prediction for GeneMark_model.9819_t
Valid prediction for snap_scaffold_3-snap.93-T1
Valid prediction for Augustus_model.g3943.t1
Valid prediction for snap_scaffold_3-snap.123-T1
Valid prediction for GlimmerHMM_glimmerT_5987-T1
Valid prediction for GeneMark_model.9792_t
Valid prediction for GeneMark_model.9820_t
Valid prediction for GeneMark_model.9804_t
Valid prediction for Augustus_model.g3940.t1
Valid prediction for snap_scaffold_3-snap.95-T1
Valid prediction for snap_scaffold_3-snap.122-T1
Valid prediction for GlimmerHMM_glimmerT_5990-T1
Valid prediction for GlimmerHMM_glimmerT_6004-T1
Valid prediction for snap_scaffold_3-snap.118-T1
Valid prediction for snap_scaffold_3-snap.114-T1
Valid prediction for GeneMark_model.9816_t
Valid prediction for Augustus_model.g3942.t1
Valid prediction for snap_scaffold_3-snap.107-T1
Valid prediction for Augustus_model.g3946.t1
Valid prediction for snap_scaffold_3-snap.112-T1
Valid prediction for GeneMark_model.9801_t
Valid prediction for GlimmerHMM_glimmerT_6003-T1
Valid prediction for GlimmerHMM_glimmerT_5994-T1
Valid prediction for GeneMark_model.9810_t
Valid prediction for snap_scaffold_3-snap.102-T1
Valid prediction for snap_scaffold_3-snap.110-T1
Valid prediction for snap_scaffold_3-snap.124-T1
Valid prediction for snap_scaffold_3-snap.98-T1
Valid prediction for snap_scaffold_3-snap.111-T1
Valid prediction for snap_scaffold_3-snap.94-T1
Valid prediction for Augustus_model.g3945.t1
Valid prediction for snap_scaffold_3-snap.117-T1
Valid prediction for snap_scaffold_3-snap.120-T1
Valid prediction for snap_scaffold_3-snap.100-T1
Valid prediction for snap_scaffold_3-snap.106-T1
Valid prediction for GlimmerHMM_glimmerT_5998-T1
Valid prediction for GeneMark_model.9822_t
Valid prediction for GeneMark_model.9799_t
Valid prediction for GeneMark_model.9808_t

-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 GeneMark_model.9814_t
Valid prediction for snap_scaffold_3-snap.105-T1
Valid prediction for GlimmerHMM_glimmerT_5986-T1
Valid prediction for GlimmerHMM_glimmerT_5999-T1
Valid prediction for GeneMark_model.9803_t
Valid prediction for GeneMark_model.9818_t
Valid prediction for snap_scaffold_3-snap.113-T1
Valid prediction for GlimmerHMM_glimmerT_5984-T1
Valid prediction for GeneMark_model.9797_t
Valid prediction for GeneMark_model.9795_t
Valid prediction for GeneMark_model.9811_t
Valid prediction for GeneMark_model.9821_t
Valid prediction for GeneMark_model.9812_t
Valid prediction for GeneMark_model.9815_t
Valid prediction for snap_scaffold_3-snap.108-T1
Valid prediction for snap_scaffold_3-snap.119-T1
Valid prediction for snap_scaffold_3-snap.97-T1
Valid prediction for Augustus_model.g3947.t1
Valid prediction for GlimmerHMM_glimmerT_6001-T1
Valid prediction for GlimmerHMM_glimmerT_6002-T1
Valid prediction for Augustus_model.g3938.t1
Valid prediction for Augustus_model.g3948.t1
Valid prediction for GlimmerHMM_glimmerT_5995-T1
Valid prediction for snap_scaffold_3-snap.104-T1
Valid prediction for snap_scaffold_3-snap.99-T1
Valid prediction for GeneMark_model.9806_t
Valid prediction for GlimmerHMM_glimmerT_5992-T1
Valid prediction for GeneMark_model.9793_t
Valid prediction for snap_scaffold_3-snap.116-T1
Valid prediction for GeneMark_model.9823_t
Valid prediction for GlimmerHMM_glimmerT_6005-T1
Valid prediction for snap_scaffold_3-snap.121-T1
Valid prediction for snap_scaffold_3-snap.115-T1
Valid prediction for GeneMark_model.9805_t
Valid prediction for GlimmerHMM_glimmerT_5993-T1
Valid prediction for GeneMark_model.9817_t
Valid prediction for GeneMark_model.9796_t
Valid prediction for Augustus_model.g3939.t1
Valid prediction for GlimmerHMM_glimmerT_5991-T1
Valid prediction for GlimmerHMM_glimmerT_5988-T1
Valid prediction for snap_scaffold_3-snap.103-T1
Valid prediction for GlimmerHMM_glimmerT_5997-T1
Valid prediction for Augustus_model.g3944.t1
Valid prediction for GeneMark_model.9809_t
Valid prediction for snap_scaffold_3-snap.101-T1
Valid prediction for snap_scaffold_3-snap.109-T1
Valid prediction for GeneMark_model.9802_t
Valid prediction for GlimmerHMM_glimmerT_5985-T1
Valid prediction for Augustus_model.g3941.t1
Valid prediction for GlimmerHMM_glimmerT_5996-T1
Valid prediction for GeneMark_model.9800_t
Valid prediction for GlimmerHMM_glimmerT_5989-T1
Valid prediction for snap_scaffold_3-snap.91-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: 38976, rend_intergenic: 34125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71775, rend_intergenic: 69435  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: 93434  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 - 133311
-exon list size: 400


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
3.0    
3.2    
3.5    
3.7    
4.0    
4.2    
4.5    
4.7    
5.0    
5.2    
5.5    
5.7    
6.0    
6.2    
6.5    
6.7    
7.0    
7.2    
7.5    
7.7    
8.0    
8.2    
8.5    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.4    
64.7    
64.9    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 22 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: 38976, rend_intergenic: 34125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71775, rend_intergenic: 69435  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: 93434  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.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 107085 - 133311
-exon list size: 53


building trellis

1.8    
3.6    
5.5    
7.3    
9.1    
10.9    
12.7    
14.5    
16.4    
18.2    
20.0    
21.8    
23.6    
25.5    
27.3    
29.1    
30.9    
32.7    
34.5    
36.4    
38.2    
40.0    
41.8    
43.6    
45.5    
47.3    
49.1    
50.9    
52.7    
54.5    
56.4    
58.2    
60.0    
61.8    
63.6    
65.5    
67.3    
69.1    
70.9    
72.7    
74.5    
76.4    
78.2    
80.0    
81.8    
83.6    
85.5    
87.3    
89.1    
90.9    
92.7    
94.5    
96.4    
98.2    
-found 3 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 117845 - 133311
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 119424 - 133311
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support