-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_15346176-15509172

-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 snap_scaffold_1-snap.2706-T1
Valid prediction for GeneMark_model.2895_t
Valid prediction for GeneMark_model.2902_t
Valid prediction for GeneMark_model.2903_t
Valid prediction for GeneMark_model.2922_t
Valid prediction for snap_scaffold_1-snap.2692-T1
Valid prediction for snap_scaffold_1-snap.2714-T1
Valid prediction for snap_scaffold_1-snap.2700-T1
Valid prediction for GlimmerHMM_glimmerT_2078-T1
Valid prediction for GeneMark_model.2913_t
Valid prediction for snap_scaffold_1-snap.2693-T1
Valid prediction for GeneMark_model.2930_t
Valid prediction for Augustus_model.g1526.t1
Valid prediction for Augustus_model.g1527.t1
Valid prediction for GlimmerHMM_glimmerT_2090-T1
Valid prediction for GlimmerHMM_glimmerT_2080-T1
Valid prediction for GeneMark_model.2891_t
Valid prediction for GeneMark_model.2888_t
Valid prediction for GeneMark_model.2933_t
Valid prediction for GlimmerHMM_glimmerT_2072-T1
Valid prediction for GeneMark_model.2919_t
Valid prediction for GeneMark_model.2932_t
Valid prediction for snap_scaffold_1-snap.2687-T1
Valid prediction for snap_scaffold_1-snap.2710-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g1531.t1
Valid prediction for snap_scaffold_1-snap.2701-T1
Valid prediction for GeneMark_model.2925_t
Valid prediction for GeneMark_model.2918_t
Valid prediction for Augustus_model.g1529.t1
Valid prediction for Augustus_model.g1528.t1
Valid prediction for GeneMark_model.2900_t
Valid prediction for GeneMark_model.2924_t
Valid prediction for GeneMark_model.2914_t
Valid prediction for GeneMark_model.2905_t
Valid prediction for Augustus_model.g1542.t1
Valid prediction for snap_scaffold_1-snap.2694-T1
Valid prediction for Augustus_model.g1532.t1
Valid prediction for Augustus_model.g1525.t1
Valid prediction for snap_scaffold_1-snap.2719-T1
Valid prediction for snap_scaffold_1-snap.2696-T1
Valid prediction for GeneMark_model.2911_t
Valid prediction for Augustus_model.g1540.t1
Valid prediction for Augustus_model.g1533.t1
Valid prediction for snap_scaffold_1-snap.2705-T1
Valid prediction for GlimmerHMM_glimmerT_2074-T1
Valid prediction for snap_scaffold_1-snap.2708-T1
Valid prediction for snap_scaffold_1-snap.2722-T1
Valid prediction for snap_scaffold_1-snap.2711-T1
Valid prediction for snap_scaffold_1-snap.2690-T1
Valid prediction for GeneMark_model.2906_t
Valid prediction for GeneMark_model.2909_t
Valid prediction for snap_scaffold_1-snap.2698-T1
Valid prediction for GlimmerHMM_glimmerT_2081-T1
Valid prediction for GeneMark_model.2894_t
Valid prediction for GlimmerHMM_glimmerT_2076-T1
Valid prediction for GlimmerHMM_glimmerT_2089-T1
Valid prediction for snap_scaffold_1-snap.2716-T1
Valid prediction for GeneMark_model.2896_t
Valid prediction for GeneMark_model.2929_t
Valid prediction for snap_scaffold_1-snap.2703-T1
Valid prediction for GlimmerHMM_glimmerT_2075-T1
Valid prediction for snap_scaffold_1-snap.2697-T1
Valid prediction for GeneMark_model.2889_t
Valid prediction for GeneMark_model.2927_t
Valid prediction for snap_scaffold_1-snap.2688-T1
Valid prediction for Augustus_model.g1524.t1
Valid prediction for Augustus_model.g1530.t1
Valid prediction for GeneMark_model.2916_t
Valid prediction for GeneMark_model.2887_t
Valid prediction for GeneMark_model.2893_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 snap_scaffold_1-snap.2717-T1
Valid prediction for Augustus_model.g1536.t1
Valid prediction for snap_scaffold_1-snap.2720-T1
Valid prediction for GeneMark_model.2923_t
Valid prediction for GlimmerHMM_glimmerT_2079-T1
Couldn't classify 59950, 59973
Sorry, prediction pasa_asmbl_964.p1 fails validation.
(CGG)	 AG	59950-59973	GT	AGG
(GAG)	 AG	60466-60612	GT	AGG
(TTG)	 AG	61763-61856	GT	CTG
(CGG)	 AG	62180-62256	GT	TGG
(GGC)	 AG	62724-62852	GT	TGG
(GCG)	 AG	63277-63423	GT	AGG
(GAT)	 AG	63641-63783	GT	GAG
(GTA)	 AG	64800-64935	GT	TGG
(GAT)	 AG	65053-65202	AG	GAA
-recovered pasa_asmbl_964.p1, terminal, 65053, 65202
-recovered pasa_asmbl_964.p1, internal, 59950, 59973
-recovered pasa_asmbl_964.p1, internal, 60466, 60612
-recovered pasa_asmbl_964.p1, internal, 61763, 61856
-recovered pasa_asmbl_964.p1, internal, 62180, 62256
-recovered pasa_asmbl_964.p1, internal, 62724, 62852
-recovered pasa_asmbl_964.p1, internal, 63277, 63423
-recovered pasa_asmbl_964.p1, internal, 63641, 63783
-recovered pasa_asmbl_964.p1, internal, 64800, 64935
Valid prediction for GeneMark_model.2898_t
Valid prediction for snap_scaffold_1-snap.2723-T1
Valid prediction for GlimmerHMM_glimmerT_2085-T1
Valid prediction for GlimmerHMM_glimmerT_2091-T1
Valid prediction for GlimmerHMM_glimmerT_2073-T1
Valid prediction for GeneMark_model.2886_t
Valid prediction for GlimmerHMM_glimmerT_2083-T1
Valid prediction for GeneMark_model.2892_t
Valid prediction for GeneMark_model.2899_t
Valid prediction for Augustus_model.g1539.t1
Valid prediction for snap_scaffold_1-snap.2709-T1
Valid prediction for snap_scaffold_1-snap.2691-T1
Valid prediction for GlimmerHMM_glimmerT_2092-T1
Valid prediction for snap_scaffold_1-snap.2702-T1
Valid prediction for GeneMark_model.2921_t
Valid prediction for GeneMark_model.2912_t
Valid prediction for CodingQuarry_transcript_2930-T1
Valid prediction for GlimmerHMM_glimmerT_2088-T1
Valid prediction for GeneMark_model.2904_t
Valid prediction for snap_scaffold_1-snap.2699-T1
Valid prediction for Augustus_model.g1543.t1
Valid prediction for GlimmerHMM_glimmerT_2087-T1
Valid prediction for snap_scaffold_1-snap.2724-T1
Valid prediction for Augustus_model.g1541.t1
Valid prediction for GeneMark_model.2901_t
Valid prediction for GlimmerHMM_glimmerT_2082-T1
Valid prediction for GeneMark_model.2931_t
Valid prediction for GlimmerHMM_glimmerT_2093-T1
Valid prediction for GeneMark_model.2917_t
Valid prediction for snap_scaffold_1-snap.2718-T1
Valid prediction for Augustus_model.g1538.t1
Valid prediction for GeneMark_model.2928_t
Valid prediction for GeneMark_model.2890_t
Valid prediction for snap_scaffold_1-snap.2721-T1
Valid prediction for GeneMark_model.2915_t
Valid prediction for GlimmerHMM_glimmerT_2084-T1
Valid prediction for snap_scaffold_1-snap.2715-T1
Valid prediction for GeneMark_model.2908_t
Valid prediction for Augustus_model.g1537.t1
Couldn't classify 68308, 68352
Sorry, prediction pasa_asmbl_963.p1 fails validation.
(CAA)	 TG	68308-68352	GT	CGG
(GAT)	 AG	68543-68611	GT	AGG
(ACA)	 AG	68918-69121	CA	GAC
-recovered pasa_asmbl_963.p1, terminal, 68918, 69121
-recovered pasa_asmbl_963.p1, internal, 68543, 68611
Valid prediction for GeneMark_model.2910_t
Valid prediction for snap_scaffold_1-snap.2713-T1
Valid prediction for GeneMark_model.2897_t
Valid prediction for GeneMark_model.2934_t
Valid prediction for snap_scaffold_1-snap.2695-T1
Valid prediction for snap_scaffold_1-snap.2707-T1
Valid prediction for GeneMark_model.2920_t
Valid prediction for GlimmerHMM_glimmerT_2077-T1
Valid prediction for GeneMark_model.2926_t
Valid prediction for Augustus_model.g1535.t1
Valid prediction for snap_scaffold_1-snap.2712-T1
Valid prediction for snap_scaffold_1-snap.2704-T1
Valid prediction for HiQ_model.g1534.t1
Valid prediction for snap_scaffold_1-snap.2689-T1
Valid prediction for GlimmerHMM_glimmerT_2086-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27041, rend_intergenic: 18574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30860, rend_intergenic: 29594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35293, rend_intergenic: 31198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45890, rend_intergenic: 42590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47753, rend_intergenic: 47327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56859, rend_intergenic: 54156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65484, rend_intergenic: 63607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74663, rend_intergenic: 69515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105772, rend_intergenic: 102109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121953, rend_intergenic: 107962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125661, rend_intergenic: 124570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130063, rend_intergenic: 126326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140008, rend_intergenic: 137272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145872, rend_intergenic: 141160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155280, rend_intergenic: 152518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162997
-exon list size: 597


building trellis

0.2    
0.3    
0.5    
0.7    
0.8    
1.0    
1.2    
1.3    
1.5    
1.7    
1.8    
2.0    
2.2    
2.3    
2.5    
2.7    
2.8    
3.0    
3.2    
3.3    
3.5    
3.7    
3.8    
4.0    
4.2    
4.3    
4.5    
4.7    
4.8    
5.0    
5.2    
5.3    
5.5    
5.7    
5.8    
6.0    
6.2    
6.3    
6.5    
6.7    
6.8    
7.0    
7.2    
7.3    
7.5    
7.7    
7.8    
8.0    
8.2    
8.3    
8.5    
8.7    
8.8    
9.0    
9.2    
9.3    
9.5    
9.7    
9.8    
10.0    
10.2    
10.4    
10.5    
10.7    
10.9    
11.0    
11.2    
11.4    
11.5    
11.7    
11.9    
12.0    
12.2    
12.4    
12.5    
12.7    
12.9    
13.0    
13.2    
13.4    
13.5    
13.7    
13.9    
14.0    
14.2    
14.4    
14.5    
14.7    
14.9    
15.0    
15.2    
15.4    
15.5    
15.7    
15.9    
16.0    
16.2    
16.4    
16.5    
16.7    
16.9    
17.0    
17.2    
17.4    
17.5    
17.7    
17.9    
18.0    
18.2    
18.4    
18.5    
18.7    
18.9    
19.0    
19.2    
19.4    
19.5    
19.7    
19.9    
20.0    
20.2    
20.4    
20.5    
20.7    
20.9    
21.0    
21.2    
21.4    
21.5    
21.7    
21.9    
22.0    
22.2    
22.4    
22.5    
22.7    
22.9    
23.0    
23.2    
23.4    
23.5    
23.7    
23.9    
24.0    
24.2    
24.4    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.5    
25.7    
25.9    
26.0    
26.2    
26.4    
26.5    
26.7    
26.9    
27.0    
27.2    
27.4    
27.5    
27.7    
27.9    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.0    
29.2    
29.4    
29.5    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.7    
31.9    
32.1    
32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.2    
33.4    
33.6    
33.7    
33.9    
34.1    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.2    
35.4    
35.6    
35.7    
35.9    
36.1    
36.2    
36.4    
36.6    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.7    
37.9    
38.1    
38.2    
38.4    
38.6    
38.7    
38.9    
39.1    
39.2    
39.4    
39.6    
39.7    
39.9    
40.1    
40.2    
40.4    
40.6    
40.7    
40.9    
41.1    
41.2    
41.4    
41.6    
41.7    
41.9    
42.1    
42.2    
42.4    
42.6    
42.7    
42.9    
43.1    
43.2    
43.4    
43.6    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.2    
46.4    
46.6    
46.7    
46.9    
47.1    
47.2    
47.4    
47.6    
47.7    
47.9    
48.1    
48.2    
48.4    
48.6    
48.7    
48.9    
49.1    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
50.9    
51.1    
51.3    
51.4    
51.6    
51.8    
51.9    
52.1    
52.3    
52.4    
52.6    
52.8    
52.9    
53.1    
53.3    
53.4    
53.6    
53.8    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.4    
58.6    
58.8    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
59.9    
60.1    
60.3    
60.4    
60.6    
60.8    
60.9    
61.1    
61.3    
61.4    
61.6    
61.8    
61.9    
62.1    
62.3    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.4    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.8    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 27041, rend_intergenic: 18574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30860, rend_intergenic: 29594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35293, rend_intergenic: 31198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45890, rend_intergenic: 42590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47753, rend_intergenic: 47327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56859, rend_intergenic: 54156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65484, rend_intergenic: 63607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74663, rend_intergenic: 69515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105772, rend_intergenic: 102109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121953, rend_intergenic: 107962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125661, rend_intergenic: 124570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130063, rend_intergenic: 126326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140008, rend_intergenic: 137272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145872, rend_intergenic: 141160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155280, rend_intergenic: 152518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support