-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_12632062-12828171

-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 GeneMark_model.49539_t
Valid prediction for GeneMark_model.49493_t
Valid prediction for GeneMark_model.49531_t
Valid prediction for GeneMark_model.49508_t
Valid prediction for GeneMark_model.49538_t
Valid prediction for GeneMark_model.49502_t
Valid prediction for GeneMark_model.49513_t
Valid prediction for GeneMark_model.49496_t
Valid prediction for GeneMark_model.49491_t
Valid prediction for snap_scaffold_11-snap.2722-T1
Valid prediction for GeneMark_model.49515_t
Valid prediction for snap_scaffold_11-snap.2725-T1
Valid prediction for snap_scaffold_11-snap.2720-T1
Valid prediction for GeneMark_model.49526_t
Valid prediction for GeneMark_model.49497_t
Valid prediction for snap_scaffold_11-snap.2752-T1
Valid prediction for Augustus_model.g19144.t1
Valid prediction for GeneMark_model.49534_t
Valid prediction for GlimmerHMM_glimmerT_28669-T1
Valid prediction for GeneMark_model.49511_t
Valid prediction for GeneMark_model.49500_t
Valid prediction for GeneMark_model.49490_t
Valid prediction for GeneMark_model.49504_t
Valid prediction for GlimmerHMM_glimmerT_28683-T1
Valid prediction for snap_scaffold_11-snap.2744-T1
Valid prediction for GeneMark_model.49536_t
Valid prediction for GeneMark_model.49533_t
Valid prediction for GlimmerHMM_glimmerT_28680-T1
Valid prediction for Augustus_model.g19142.t1
Valid prediction for snap_scaffold_11-snap.2743-T1
Valid prediction for GlimmerHMM_glimmerT_28688-T1
Valid prediction for GlimmerHMM_glimmerT_28677-T1
Valid prediction for GeneMark_model.49541_t
Valid prediction for GlimmerHMM_glimmerT_28681-T1
Valid prediction for snap_scaffold_11-snap.2751-T1
Valid prediction for GeneMark_model.49528_t
Valid prediction for snap_scaffold_11-snap.2727-T1
Valid prediction for snap_scaffold_11-snap.2747-T1
Valid prediction for GeneMark_model.49518_t
Valid prediction for GlimmerHMM_glimmerT_28684-T1
Valid prediction for snap_scaffold_11-snap.2728-T1
Valid prediction for snap_scaffold_11-snap.2740-T1
Valid prediction for snap_scaffold_11-snap.2738-T1
Valid prediction for snap_scaffold_11-snap.2736-T1
Valid prediction for GeneMark_model.49520_t
Valid prediction for snap_scaffold_11-snap.2734-T1
Valid prediction for GlimmerHMM_glimmerT_28670-T1
Valid prediction for GeneMark_model.49529_t
Valid prediction for GlimmerHMM_glimmerT_28685-T1
Valid prediction for snap_scaffold_11-snap.2730-T1
Valid prediction for GeneMark_model.49524_t
Valid prediction for snap_scaffold_11-snap.2748-T1
Valid prediction for GeneMark_model.49506_t
Valid prediction for GeneMark_model.49488_t
Valid prediction for GlimmerHMM_glimmerT_28668-T1
Valid prediction for snap_scaffold_11-snap.2733-T1
Valid prediction for GlimmerHMM_glimmerT_28671-T1
Valid prediction for Augustus_model.g19138.t1
Valid prediction for GeneMark_model.49521_t
Valid prediction for GlimmerHMM_glimmerT_28686-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_11-snap.2745-T1
Valid prediction for snap_scaffold_11-snap.2753-T1
Valid prediction for CodingQuarry_transcript_8240-T1
Valid prediction for Augustus_model.g19145.t1
Valid prediction for Augustus_model.g19140.t1
Valid prediction for GeneMark_model.49522_t
Valid prediction for snap_scaffold_11-snap.2729-T1
Valid prediction for GlimmerHMM_glimmerT_28676-T1
Valid prediction for GeneMark_model.49519_t
Valid prediction for GeneMark_model.49492_t
Valid prediction for GlimmerHMM_glimmerT_28678-T1
Valid prediction for Augustus_model.g19139.t1
Valid prediction for GeneMark_model.49516_t
Valid prediction for snap_scaffold_11-snap.2731-T1
Valid prediction for snap_scaffold_11-snap.2739-T1
Valid prediction for GeneMark_model.49523_t
Valid prediction for GeneMark_model.49517_t
Valid prediction for CodingQuarry_transcript_8239-T1
Valid prediction for GeneMark_model.49495_t
Valid prediction for GlimmerHMM_glimmerT_28667-T1
Valid prediction for snap_scaffold_11-snap.2741-T1
Couldn't classify 153721, 154023
Sorry, prediction pasa_asmbl_7074.p1 fails validation.
(CTA)	 CT	153721-154023	TA	AGT
Valid prediction for snap_scaffold_11-snap.2724-T1
Valid prediction for snap_scaffold_11-snap.2746-T1
Valid prediction for GlimmerHMM_glimmerT_28679-T1
Valid prediction for snap_scaffold_11-snap.2750-T1
Valid prediction for GeneMark_model.49505_t
Valid prediction for GlimmerHMM_glimmerT_28673-T1
Valid prediction for Augustus_model.g19146.t1
Valid prediction for snap_scaffold_11-snap.2749-T1
Valid prediction for GlimmerHMM_glimmerT_28672-T1
Valid prediction for GeneMark_model.49503_t
Valid prediction for GeneMark_model.49507_t
Valid prediction for snap_scaffold_11-snap.2737-T1
Valid prediction for GlimmerHMM_glimmerT_28674-T1
Valid prediction for GeneMark_model.49530_t
Valid prediction for GeneMark_model.49535_t
Valid prediction for snap_scaffold_11-snap.2723-T1
Valid prediction for snap_scaffold_11-snap.2721-T1
Valid prediction for GeneMark_model.49487_t
Valid prediction for Augustus_model.g19137.t1
Valid prediction for Augustus_model.g19143.t1
Valid prediction for snap_scaffold_11-snap.2732-T1
Valid prediction for snap_scaffold_11-snap.2735-T1
Valid prediction for GeneMark_model.49501_t
Valid prediction for GeneMark_model.49512_t
Valid prediction for GlimmerHMM_glimmerT_28682-T1
Valid prediction for GeneMark_model.49498_t
Valid prediction for GeneMark_model.49499_t
Valid prediction for GeneMark_model.49510_t
Valid prediction for GeneMark_model.49525_t
Valid prediction for GeneMark_model.49509_t
Valid prediction for GeneMark_model.49540_t
Valid prediction for Augustus_model.g19136.t1
Valid prediction for GeneMark_model.49486_t
Valid prediction for Augustus_model.g19141.t1
Valid prediction for GlimmerHMM_glimmerT_28687-T1
Valid prediction for snap_scaffold_11-snap.2726-T1
Valid prediction for GeneMark_model.49514_t
Valid prediction for snap_scaffold_11-snap.2742-T1
Valid prediction for GeneMark_model.49489_t
Valid prediction for GeneMark_model.49537_t
Valid prediction for GlimmerHMM_glimmerT_28675-T1
Valid prediction for GeneMark_model.49494_t
Valid prediction for GeneMark_model.49527_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24811, rend_intergenic: 16705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30169, rend_intergenic: 26979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45323, rend_intergenic: 43312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53951, rend_intergenic: 48308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62307, rend_intergenic: 56107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74129, rend_intergenic: 67960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78169, rend_intergenic: 75065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80457, rend_intergenic: 79508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90247, rend_intergenic: 82637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94471, rend_intergenic: 91685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103623, rend_intergenic: 96527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119965, rend_intergenic: 109911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146308, rend_intergenic: 144506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196110
-exon list size: 631


building trellis

0.2    
0.3    
0.5    
0.6    
0.8    
0.9    
1.1    
1.3    
1.4    
1.6    
1.7    
1.9    
2.1    
2.2    
2.4    
2.5    
2.7    
2.8    
3.0    
3.2    
3.3    
3.5    
3.6    
3.8    
3.9    
4.1    
4.3    
4.4    
4.6    
4.7    
4.9    
5.1    
5.2    
5.4    
5.5    
5.7    
5.8    
6.0    
6.2    
6.3    
6.5    
6.6    
6.8    
7.0    
7.1    
7.3    
7.4    
7.6    
7.7    
7.9    
8.1    
8.2    
8.4    
8.5    
8.7    
8.8    
9.0    
9.2    
9.3    
9.5    
9.6    
9.8    
10.0    
10.1    
10.3    
10.4    
10.6    
10.7    
10.9    
11.1    
11.2    
11.4    
11.5    
11.7    
11.8    
12.0    
12.2    
12.3    
12.5    
12.6    
12.8    
13.0    
13.1    
13.3    
13.4    
13.6    
13.7    
13.9    
14.1    
14.2    
14.4    
14.5    
14.7    
14.8    
15.0    
15.2    
15.3    
15.5    
15.6    
15.8    
16.0    
16.1    
16.3    
16.4    
16.6    
16.7    
16.9    
17.1    
17.2    
17.4    
17.5    
17.7    
17.9    
18.0    
18.2    
18.3    
18.5    
18.6    
18.8    
19.0    
19.1    
19.3    
19.4    
19.6    
19.7    
19.9    
20.1    
20.2    
20.4    
20.5    
20.7    
20.9    
21.0    
21.2    
21.3    
21.5    
21.6    
21.8    
22.0    
22.1    
22.3    
22.4    
22.6    
22.7    
22.9    
23.1    
23.2    
23.4    
23.5    
23.7    
23.9    
24.0    
24.2    
24.3    
24.5    
24.6    
24.8    
25.0    
25.1    
25.3    
25.4    
25.6    
25.8    
25.9    
26.1    
26.2    
26.4    
26.5    
26.7    
26.9    
27.0    
27.2    
27.3    
27.5    
27.6    
27.8    
28.0    
28.1    
28.3    
28.4    
28.6    
28.8    
28.9    
29.1    
29.2    
29.4    
29.5    
29.7    
29.9    
30.0    
30.2    
30.3    
30.5    
30.6    
30.8    
31.0    
31.1    
31.3    
31.4    
31.6    
31.8    
31.9    
32.1    
32.2    
32.4    
32.5    
32.7    
32.9    
33.0    
33.2    
33.3    
33.5    
33.6    
33.8    
34.0    
34.1    
34.3    
34.4    
34.6    
34.8    
34.9    
35.1    
35.2    
35.4    
35.5    
35.7    
35.9    
36.0    
36.2    
36.3    
36.5    
36.7    
36.8    
37.0    
37.1    
37.3    
37.4    
37.6    
37.8    
37.9    
38.1    
38.2    
38.4    
38.5    
38.7    
38.9    
39.0    
39.2    
39.3    
39.5    
39.7    
39.8    
40.0    
40.1    
40.3    
40.4    
40.6    
40.8    
40.9    
41.1    
41.2    
41.4    
41.5    
41.7    
41.9    
42.0    
42.2    
42.3    
42.5    
42.7    
42.8    
43.0    
43.1    
43.3    
43.4    
43.6    
43.8    
43.9    
44.1    
44.2    
44.4    
44.5    
44.7    
44.9    
45.0    
45.2    
45.3    
45.5    
45.7    
45.8    
46.0    
46.1    
46.3    
46.4    
46.6    
46.8    
46.9    
47.1    
47.2    
47.4    
47.6    
47.7    
47.9    
48.0    
48.2    
48.3    
48.5    
48.7    
48.8    
49.0    
49.1    
49.3    
49.4    
49.6    
49.8    
49.9    
50.1    
50.2    
50.4    
50.6    
50.7    
50.9    
51.0    
51.2    
51.3    
51.5    
51.7    
51.8    
52.0    
52.1    
52.3    
52.4    
52.6    
52.8    
52.9    
53.1    
53.2    
53.4    
53.6    
53.7    
53.9    
54.0    
54.2    
54.3    
54.5    
54.7    
54.8    
55.0    
55.1    
55.3    
55.5    
55.6    
55.8    
55.9    
56.1    
56.2    
56.4    
56.6    
56.7    
56.9    
57.0    
57.2    
57.3    
57.5    
57.7    
57.8    
58.0    
58.1    
58.3    
58.5    
58.6    
58.8    
58.9    
59.1    
59.2    
59.4    
59.6    
59.7    
59.9    
60.0    
60.2    
60.3    
60.5    
60.7    
60.8    
61.0    
61.1    
61.3    
61.5    
61.6    
61.8    
61.9    
62.1    
62.2    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.7    
63.8    
64.0    
64.1    
64.3    
64.5    
64.6    
64.8    
64.9    
65.1    
65.2    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.4    
66.5    
66.7    
66.8    
67.0    
67.1    
67.3    
67.5    
67.6    
67.8    
67.9    
68.1    
68.2    
68.4    
68.6    
68.7    
68.9    
69.0    
69.2    
69.4    
69.5    
69.7    
69.8    
70.0    
70.1    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.2    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.3    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.8    
76.0    
76.1    
76.3    
76.5    
76.6    
76.8    
76.9    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 24811, rend_intergenic: 16705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30169, rend_intergenic: 26979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45323, rend_intergenic: 43312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53951, rend_intergenic: 48308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62307, rend_intergenic: 56107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74129, rend_intergenic: 67960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78169, rend_intergenic: 75065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80457, rend_intergenic: 79508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90247, rend_intergenic: 82637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94471, rend_intergenic: 91685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103623, rend_intergenic: 96527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119965, rend_intergenic: 109911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146308, rend_intergenic: 144506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 8 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 169019 - 196110
-exon list size: 37


building trellis

2.6    
5.1    
7.7    
10.3    
12.8    
15.4    
17.9    
20.5    
23.1    
25.6    
28.2    
30.8    
33.3    
35.9    
38.5    
41.0    
43.6    
46.2    
48.7    
51.3    
53.8    
56.4    
59.0    
61.5    
64.1    
66.7    
69.2    
71.8    
74.4    
76.9    
79.5    
82.1    
84.6    
87.2    
89.7    
92.3    
94.9    
97.4    
-found 1 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 169019 - 183225
-exon list size: 29


building trellis

3.2    
6.5    
9.7    
12.9    
16.1    
19.4    
22.6    
25.8    
29.0    
32.3    
35.5    
38.7    
41.9    
45.2    
48.4    
51.6    
54.8    
58.1    
61.3    
64.5    
67.7    
71.0    
74.2    
77.4    
80.6    
83.9    
87.1    
90.3    
93.5    
96.8    
-found 1 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 169019 - 181788
-exon list size: 23


building trellis

4.0    
8.0    
12.0    
16.0    
20.0    
24.0    
28.0    
32.0    
36.0    
40.0    
44.0    
48.0    
52.0    
56.0    
60.0    
64.0    
68.0    
72.0    
76.0    
80.0    
84.0    
88.0    
92.0    
96.0    
-found 1 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 183258 - 196110
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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