-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_19576543-19789818

-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_8530-T1
Valid prediction for GlimmerHMM_glimmerT_8551-T1
Valid prediction for GlimmerHMM_glimmerT_8538-T1
Valid prediction for snap_scaffold_3-snap.3877-T1
Valid prediction for snap_scaffold_3-snap.3893-T1
Valid prediction for snap_scaffold_3-snap.3894-T1
Valid prediction for snap_scaffold_3-snap.3871-T1
Valid prediction for GlimmerHMM_glimmerT_8543-T1
Valid prediction for GlimmerHMM_glimmerT_8542-T1
Valid prediction for snap_scaffold_3-snap.3880-T1
Valid prediction for GlimmerHMM_glimmerT_8535-T1
Valid prediction for snap_scaffold_3-snap.3906-T1
Valid prediction for snap_scaffold_3-snap.3884-T1
Valid prediction for snap_scaffold_3-snap.3866-T1
Valid prediction for snap_scaffold_3-snap.3912-T1
Valid prediction for snap_scaffold_3-snap.3899-T1
Valid prediction for GlimmerHMM_glimmerT_8531-T1
Valid prediction for GlimmerHMM_glimmerT_8528-T1
Valid prediction for GlimmerHMM_glimmerT_8544-T1
Valid prediction for snap_scaffold_3-snap.3870-T1
Valid prediction for snap_scaffold_3-snap.3910-T1
Valid prediction for GlimmerHMM_glimmerT_8539-T1
Valid prediction for GlimmerHMM_glimmerT_8548-T1
Valid prediction for GlimmerHMM_glimmerT_8534-T1
Valid prediction for snap_scaffold_3-snap.3887-T1
Valid prediction for snap_scaffold_3-snap.3890-T1
Valid prediction for snap_scaffold_3-snap.3874-T1
Valid prediction for snap_scaffold_3-snap.3896-T1
Valid prediction for snap_scaffold_3-snap.3873-T1
Valid prediction for snap_scaffold_3-snap.3888-T1
Valid prediction for snap_scaffold_3-snap.3904-T1
Valid prediction for snap_scaffold_3-snap.3914-T1
Valid prediction for snap_scaffold_3-snap.3881-T1
Valid prediction for GlimmerHMM_glimmerT_8533-T1
Valid prediction for snap_scaffold_3-snap.3907-T1
Valid prediction for GlimmerHMM_glimmerT_8526-T1
Valid prediction for GlimmerHMM_glimmerT_8527-T1
Valid prediction for snap_scaffold_3-snap.3879-T1
Valid prediction for GlimmerHMM_glimmerT_8532-T1
Valid prediction for GlimmerHMM_glimmerT_8552-T1
Valid prediction for snap_scaffold_3-snap.3883-T1
Valid prediction for snap_scaffold_3-snap.3867-T1
Valid prediction for snap_scaffold_3-snap.3895-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.3886-T1
Valid prediction for snap_scaffold_3-snap.3908-T1
Valid prediction for snap_scaffold_3-snap.3868-T1
Valid prediction for snap_scaffold_3-snap.3869-T1
Valid prediction for snap_scaffold_3-snap.3885-T1
Valid prediction for GlimmerHMM_glimmerT_8550-T1
Valid prediction for snap_scaffold_3-snap.3909-T1
Valid prediction for snap_scaffold_3-snap.3900-T1
Valid prediction for GlimmerHMM_glimmerT_8541-T1
Valid prediction for snap_scaffold_3-snap.3875-T1
Valid prediction for snap_scaffold_3-snap.3897-T1
Valid prediction for snap_scaffold_3-snap.3891-T1
Valid prediction for GlimmerHMM_glimmerT_8537-T1
Valid prediction for snap_scaffold_3-snap.3911-T1
Valid prediction for snap_scaffold_3-snap.3915-T1
Valid prediction for snap_scaffold_3-snap.3901-T1
Valid prediction for snap_scaffold_3-snap.3878-T1
Valid prediction for GlimmerHMM_glimmerT_8545-T1
Valid prediction for GlimmerHMM_glimmerT_8549-T1
Valid prediction for GlimmerHMM_glimmerT_8536-T1
Valid prediction for snap_scaffold_3-snap.3882-T1
Valid prediction for snap_scaffold_3-snap.3905-T1
Valid prediction for GlimmerHMM_glimmerT_8547-T1
Valid prediction for GlimmerHMM_glimmerT_8546-T1
Valid prediction for GlimmerHMM_glimmerT_8529-T1
Valid prediction for snap_scaffold_3-snap.3898-T1
Valid prediction for snap_scaffold_3-snap.3903-T1
Valid prediction for snap_scaffold_3-snap.3902-T1
Valid prediction for GlimmerHMM_glimmerT_8540-T1
Valid prediction for snap_scaffold_3-snap.3872-T1
Valid prediction for snap_scaffold_3-snap.3892-T1
Valid prediction for snap_scaffold_3-snap.3876-T1
Valid prediction for snap_scaffold_3-snap.3913-T1
Valid prediction for snap_scaffold_3-snap.3889-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 124939, rend_intergenic: 124936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23735, rend_intergenic: 19070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31889, rend_intergenic: 27988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45592, rend_intergenic: 43910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53682, rend_intergenic: 51052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66835, rend_intergenic: 61286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93441, rend_intergenic: 90309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100188, rend_intergenic: 96965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112890, rend_intergenic: 108526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116117, rend_intergenic: 112958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140135, rend_intergenic: 132700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156616, rend_intergenic: 154612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173842, rend_intergenic: 159670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192818, rend_intergenic: 186476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199468, rend_intergenic: 198333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201876, rend_intergenic: 201120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211580, rend_intergenic: 204442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213276
-exon list size: 265


building trellis

0.4    
0.7    
1.1    
1.5    
1.9    
2.2    
2.6    
3.0    
3.4    
3.7    
4.1    
4.5    
4.9    
5.2    
5.6    
6.0    
6.4    
6.7    
7.1    
7.5    
7.9    
8.2    
8.6    
9.0    
9.4    
9.7    
10.1    
10.5    
10.9    
11.2    
11.6    
12.0    
12.4    
12.7    
13.1    
13.5    
13.9    
14.2    
14.6    
15.0    
15.4    
15.7    
16.1    
16.5    
16.9    
17.2    
17.6    
18.0    
18.4    
18.7    
19.1    
19.5    
19.9    
20.2    
20.6    
21.0    
21.3    
21.7    
22.1    
22.5    
22.8    
23.2    
23.6    
24.0    
24.3    
24.7    
25.1    
25.5    
25.8    
26.2    
26.6    
27.0    
27.3    
27.7    
28.1    
28.5    
28.8    
29.2    
29.6    
30.0    
30.3    
30.7    
31.1    
31.5    
31.8    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.5    
34.8    
35.2    
35.6    
36.0    
36.3    
36.7    
37.1    
37.5    
37.8    
38.2    
38.6    
39.0    
39.3    
39.7    
40.1    
40.4    
40.8    
41.2    
41.6    
41.9    
42.3    
42.7    
43.1    
43.4    
43.8    
44.2    
44.6    
44.9    
45.3    
45.7    
46.1    
46.4    
46.8    
47.2    
47.6    
47.9    
48.3    
48.7    
49.1    
49.4    
49.8    
50.2    
50.6    
50.9    
51.3    
51.7    
52.1    
52.4    
52.8    
53.2    
53.6    
53.9    
54.3    
54.7    
55.1    
55.4    
55.8    
56.2    
56.6    
56.9    
57.3    
57.7    
58.1    
58.4    
58.8    
59.2    
59.6    
59.9    
60.3    
60.7    
61.0    
61.4    
61.8    
62.2    
62.5    
62.9    
63.3    
63.7    
64.0    
64.4    
64.8    
65.2    
65.5    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.2    
68.5    
68.9    
69.3    
69.7    
70.0    
70.4    
70.8    
71.2    
71.5    
71.9    
72.3    
72.7    
73.0    
73.4    
73.8    
74.2    
74.5    
74.9    
75.3    
75.7    
76.0    
76.4    
76.8    
77.2    
77.5    
77.9    
78.3    
78.7    
79.0    
79.4    
79.8    
80.1    
80.5    
80.9    
81.3    
81.6    
82.0    
82.4    
82.8    
83.1    
83.5    
83.9    
84.3    
84.6    
85.0    
85.4    
85.8    
86.1    
86.5    
86.9    
87.3    
87.6    
88.0    
88.4    
88.8    
89.1    
89.5    
89.9    
90.3    
90.6    
91.0    
91.4    
91.8    
92.1    
92.5    
92.9    
93.3    
93.6    
94.0    
94.4    
94.8    
95.1    
95.5    
95.9    
96.3    
96.6    
97.0    
97.4    
97.8    
98.1    
98.5    
98.9    
99.3    
99.6    
-found 34 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 124939, rend_intergenic: 124936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23735, rend_intergenic: 19070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31889, rend_intergenic: 27988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45592, rend_intergenic: 43910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53682, rend_intergenic: 51052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66835, rend_intergenic: 61286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93441, rend_intergenic: 90309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100188, rend_intergenic: 96965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112890, rend_intergenic: 108526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116117, rend_intergenic: 112958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140135, rend_intergenic: 132700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156616, rend_intergenic: 154612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173842, rend_intergenic: 159670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192818, rend_intergenic: 186476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199468, rend_intergenic: 198333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201876, rend_intergenic: 201120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211580, rend_intergenic: 204442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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