-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_15948411-16167664

-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_4-snap.3225-T1
Valid prediction for Augustus_model.g7087.t1
Valid prediction for snap_scaffold_4-snap.3250-T1
Valid prediction for GlimmerHMM_glimmerT_10794-T1
Valid prediction for snap_scaffold_4-snap.3237-T1
Valid prediction for GlimmerHMM_glimmerT_10814-T1
Valid prediction for GlimmerHMM_glimmerT_10798-T1
Valid prediction for snap_scaffold_4-snap.3248-T1
Valid prediction for GlimmerHMM_glimmerT_10797-T1
Valid prediction for snap_scaffold_4-snap.3236-T1
Valid prediction for snap_scaffold_4-snap.3232-T1
Valid prediction for snap_scaffold_4-snap.3228-T1
Valid prediction for Augustus_model.g7083.t1
Valid prediction for snap_scaffold_4-snap.3222-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3226-T1
Valid prediction for GlimmerHMM_glimmerT_10808-T1
Valid prediction for snap_scaffold_4-snap.3243-T1
Valid prediction for CodingQuarry_transcript_49266-T1
Valid prediction for snap_scaffold_4-snap.3242-T1
Valid prediction for GlimmerHMM_glimmerT_10802-T1
Valid prediction for pasa_asmbl_41959.p1
Valid prediction for GlimmerHMM_glimmerT_10812-T1
Valid prediction for GlimmerHMM_glimmerT_10792-T1
Valid prediction for snap_scaffold_4-snap.3229-T1
Valid prediction for GlimmerHMM_glimmerT_10817-T1
Valid prediction for snap_scaffold_4-snap.3216-T1
Valid prediction for GlimmerHMM_glimmerT_10807-T1
Valid prediction for snap_scaffold_4-snap.3230-T1
Valid prediction for GlimmerHMM_glimmerT_10795-T1
Valid prediction for snap_scaffold_4-snap.3218-T1
Valid prediction for GlimmerHMM_glimmerT_10810-T1
Valid prediction for CodingQuarry_transcript_49265-T1
Valid prediction for snap_scaffold_4-snap.3233-T1
Valid prediction for snap_scaffold_4-snap.3219-T1
Valid prediction for HiQ_model.g7094.t1
Valid prediction for snap_scaffold_4-snap.3234-T1
Valid prediction for GlimmerHMM_glimmerT_10809-T1
Valid prediction for snap_scaffold_4-snap.3240-T1
Valid prediction for GlimmerHMM_glimmerT_10806-T1
Valid prediction for snap_scaffold_4-snap.3238-T1
Valid prediction for Augustus_model.g7086.t1
Valid prediction for snap_scaffold_4-snap.3253-T1
Valid prediction for snap_scaffold_4-snap.3220-T1
Valid prediction for snap_scaffold_4-snap.3252-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 HiQ_model.g7093.t1
Valid prediction for GlimmerHMM_glimmerT_10804-T1
Valid prediction for pasa_asmbl_43140.p1
Valid prediction for snap_scaffold_4-snap.3244-T1
Valid prediction for Augustus_model.g7090.t1
Valid prediction for GlimmerHMM_glimmerT_10813-T1
Valid prediction for snap_scaffold_4-snap.3227-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10816-T1
Valid prediction for Augustus_model.g7082.t1
Valid prediction for GlimmerHMM_glimmerT_10799-T1
Valid prediction for Augustus_model.g7092.t1
Valid prediction for Augustus_model.g7085.t1
Valid prediction for snap_scaffold_4-snap.3224-T1
Valid prediction for Augustus_model.g7091.t1
Valid prediction for Augustus_model.g7084.t1
Valid prediction for snap_scaffold_4-snap.3221-T1
Valid prediction for Augustus_model.g7088.t1
Valid prediction for snap_scaffold_4-snap.3246-T1
Valid prediction for Augustus_model.g7095.t1
Valid prediction for snap_scaffold_4-snap.3223-T1
Valid prediction for CodingQuarry_transcript_49263-T1
Valid prediction for snap_scaffold_4-snap.3241-T1
Valid prediction for GlimmerHMM_glimmerT_10800-T1
Valid prediction for snap_scaffold_4-snap.3249-T1
Valid prediction for GlimmerHMM_glimmerT_10801-T1
Valid prediction for GlimmerHMM_glimmerT_10811-T1
Valid prediction for GlimmerHMM_glimmerT_10793-T1
Valid prediction for CodingQuarry_transcript_49264-T1
Valid prediction for GlimmerHMM_glimmerT_10791-T1
Couldn't classify 17967, 18138
Couldn't classify 18874, 18891
Sorry, prediction pasa_asmbl_43525.p1 fails validation.
(CAG)	 TG	17967-18138	GT	GGG
(GTC)	 AG	18530-18684	GT	TGG
(GTC)	 AG	18874-18891	GC	TGG
-recovered pasa_asmbl_43525.p1, internal, 18530, 18684
-recovered pasa_asmbl_43525.p1, internal, 18874, 18891
Valid prediction for snap_scaffold_4-snap.3235-T1
Valid prediction for snap_scaffold_4-snap.3239-T1
Valid prediction for snap_scaffold_4-snap.3231-T1
Valid prediction for snap_scaffold_4-snap.3245-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 39638, 39993
Sorry, prediction pasa_asmbl_43138.p2 fails validation.
(CAC)	 AG	39638-39993	GT	AGG
(GTC)	 AG	40321-40327	TC	GAT
-recovered pasa_asmbl_43138.p2, terminal, 40321, 40327
-recovered pasa_asmbl_43138.p2, internal, 39638, 39993
Valid prediction for GlimmerHMM_glimmerT_10815-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10803-T1
Valid prediction for snap_scaffold_4-snap.3217-T1
Valid prediction for GlimmerHMM_glimmerT_10796-T1
Valid prediction for snap_scaffold_4-snap.3251-T1
Valid prediction for Augustus_model.g7089.t1
Valid prediction for GlimmerHMM_glimmerT_10805-T1
Valid prediction for snap_scaffold_4-snap.3247-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10458, rend_intergenic: 7322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11411, rend_intergenic: 10924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32928, rend_intergenic: 28454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45185, rend_intergenic: 32928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51653, rend_intergenic: 46034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60300, rend_intergenic: 51799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65810, rend_intergenic: 60412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81098, rend_intergenic: 66062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89561, rend_intergenic: 86652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92077, rend_intergenic: 90117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108921, rend_intergenic: 103076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138913, rend_intergenic: 109052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150767, rend_intergenic: 142693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154761, rend_intergenic: 153651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166236, rend_intergenic: 158133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214232, rend_intergenic: 199921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219254
-exon list size: 352


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.9    
23.2    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.8    
27.1    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.9    
73.2    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.8    
77.1    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 10458, rend_intergenic: 7322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11411, rend_intergenic: 10924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32928, rend_intergenic: 28454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45185, rend_intergenic: 32928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51653, rend_intergenic: 46034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60300, rend_intergenic: 51799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65810, rend_intergenic: 60412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81098, rend_intergenic: 66062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89561, rend_intergenic: 86652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92077, rend_intergenic: 90117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108921, rend_intergenic: 103076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138913, rend_intergenic: 109052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150767, rend_intergenic: 142693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154761, rend_intergenic: 153651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166236, rend_intergenic: 158133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214232, rend_intergenic: 199921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support