-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_492256-623143

-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_3-snap.137-T1
Valid prediction for GeneMark_model.9832_t
Valid prediction for GeneMark_model.9847_t
Valid prediction for GlimmerHMM_glimmerT_6021-T1
Valid prediction for snap_scaffold_3-snap.124-T1
Valid prediction for GeneMark_model.9830_t
Valid prediction for snap_scaffold_3-snap.143-T1
Valid prediction for HiQ_model.g3954.t1
Valid prediction for Augustus_model.g3956.t1
Valid prediction for snap_scaffold_3-snap.133-T1
Valid prediction for snap_scaffold_3-snap.138-T1
Valid prediction for Augustus_model.g3952.t1
Valid prediction for GlimmerHMM_glimmerT_6023-T1
Valid prediction for snap_scaffold_3-snap.145-T1
Valid prediction for CodingQuarry_transcript_45949-T1
Valid prediction for GlimmerHMM_glimmerT_6017-T1
Valid prediction for GeneMark_model.9856_t
Valid prediction for snap_scaffold_3-snap.126-T1
Valid prediction for GlimmerHMM_glimmerT_6020-T1
Valid prediction for snap_scaffold_3-snap.153-T1
Valid prediction for GeneMark_model.9850_t
Valid prediction for GeneMark_model.9854_t
Valid prediction for GeneMark_model.9858_t
Valid prediction for GeneMark_model.9852_t
Valid prediction for snap_scaffold_3-snap.142-T1
Valid prediction for GlimmerHMM_glimmerT_6022-T1
Valid prediction for snap_scaffold_3-snap.141-T1
Valid prediction for snap_scaffold_3-snap.129-T1
Valid prediction for pasa_asmbl_39767.p1
Valid prediction for GeneMark_model.9862_t
Valid prediction for GeneMark_model.9828_t
Valid prediction for snap_scaffold_3-snap.150-T1
Valid prediction for GlimmerHMM_glimmerT_6007-T1
Valid prediction for snap_scaffold_3-snap.127-T1
Valid prediction for snap_scaffold_3-snap.149-T1
Valid prediction for GeneMark_model.9836_t
Valid prediction for GeneMark_model.9845_t
Valid prediction for snap_scaffold_3-snap.152-T1
Valid prediction for snap_scaffold_3-snap.144-T1
Valid prediction for Augustus_model.g3955.t1
Valid prediction for GlimmerHMM_glimmerT_6009-T1
Valid prediction for snap_scaffold_3-snap.158-T1
Valid prediction for GeneMark_model.9834_t
Valid prediction for CodingQuarry_transcript_45950-T1
Valid prediction for GeneMark_model.9826_t
Valid prediction for GeneMark_model.9841_t
Valid prediction for snap_scaffold_3-snap.151-T1
Valid prediction for GlimmerHMM_glimmerT_6013-T1
Valid prediction for snap_scaffold_3-snap.136-T1
Valid prediction for GlimmerHMM_glimmerT_6014-T1
Valid prediction for GeneMark_model.9848_t
Valid prediction for snap_scaffold_3-snap.131-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.139-T1
Valid prediction for GlimmerHMM_glimmerT_6026-T1
Couldn't classify 6600, 6632
Sorry, prediction pasa_asmbl_38625.p1 fails validation.
(GTC)	 TG	6600-6632	GT	AGG
(TAC)	 AG	7241-7450	GT	AGG
(GCC)	 AG	8008-8097	GT	AGG
(GAG)	 AG	9917-10021	GT	CGG
(CCT)	 AG	10904-10921	TC	GAT
-recovered pasa_asmbl_38625.p1, terminal, 10904, 10921
-recovered pasa_asmbl_38625.p1, internal, 7241, 7450
-recovered pasa_asmbl_38625.p1, internal, 8008, 8097
-recovered pasa_asmbl_38625.p1, internal, 9917, 10021
Valid prediction for snap_scaffold_3-snap.154-T1
Valid prediction for GlimmerHMM_glimmerT_6010-T1
Valid prediction for GlimmerHMM_glimmerT_6019-T1
Valid prediction for snap_scaffold_3-snap.135-T1
Valid prediction for GeneMark_model.9825_t
Valid prediction for GeneMark_model.9853_t
Couldn't classify 16018, 16223
Sorry, prediction pasa_asmbl_38623.p1 fails validation.
(TTC)	 TG	16018-16223	GT	AGG
(TGT)	 AG	16783-17122	GA	GAG
-recovered pasa_asmbl_38623.p1, terminal, 16783, 17122
Valid prediction for GeneMark_model.9840_t
Valid prediction for snap_scaffold_3-snap.125-T1
Valid prediction for GlimmerHMM_glimmerT_6008-T1
Valid prediction for GeneMark_model.9843_t
Valid prediction for Augustus_model.g3957.t1
Valid prediction for GeneMark_model.9837_t
Valid prediction for snap_scaffold_3-snap.148-T1
Valid prediction for Augustus_model.g3958.t1
Valid prediction for GeneMark_model.9855_t
Valid prediction for snap_scaffold_3-snap.147-T1
Valid prediction for GeneMark_model.9842_t
Valid prediction for GeneMark_model.9835_t
Valid prediction for Augustus_model.g3960.t1
Valid prediction for GeneMark_model.9849_t
Valid prediction for snap_scaffold_3-snap.157-T1
Valid prediction for snap_scaffold_3-snap.146-T1
Valid prediction for GlimmerHMM_glimmerT_6012-T1
Valid prediction for GlimmerHMM_glimmerT_6011-T1
Valid prediction for GeneMark_model.9846_t
Valid prediction for GeneMark_model.9833_t
Valid prediction for GlimmerHMM_glimmerT_6025-T1
Valid prediction for Augustus_model.g3951.t1
Valid prediction for snap_scaffold_3-snap.128-T1
Valid prediction for GeneMark_model.9831_t
Valid prediction for snap_scaffold_3-snap.132-T1
Valid prediction for snap_scaffold_3-snap.155-T1
Valid prediction for snap_scaffold_3-snap.159-T1
Valid prediction for GeneMark_model.9857_t
Valid prediction for snap_scaffold_3-snap.134-T1
Valid prediction for GeneMark_model.9827_t
Valid prediction for Augustus_model.g3950.t1
Valid prediction for GlimmerHMM_glimmerT_6018-T1
Valid prediction for Augustus_model.g3953.t1
Valid prediction for GlimmerHMM_glimmerT_6016-T1
Valid prediction for GeneMark_model.9844_t
Valid prediction for GeneMark_model.9860_t
Valid prediction for GeneMark_model.9839_t
Valid prediction for GeneMark_model.9861_t
Valid prediction for GlimmerHMM_glimmerT_6024-T1
Valid prediction for snap_scaffold_3-snap.140-T1
Valid prediction for GeneMark_model.9824_t
Valid prediction for GeneMark_model.9838_t
Valid prediction for snap_scaffold_3-snap.156-T1
Valid prediction for GlimmerHMM_glimmerT_6015-T1
Valid prediction for snap_scaffold_3-snap.130-T1
Valid prediction for GeneMark_model.9829_t
Valid prediction for HiQ_model.g3959.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21687, rend_intergenic: 18269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26135, rend_intergenic: 22835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35062, rend_intergenic: 32916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43080, rend_intergenic: 38778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69230, rend_intergenic: 66094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95369, rend_intergenic: 88849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98254, rend_intergenic: 96937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126269, rend_intergenic: 124354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128257, rend_intergenic: 126715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 130888
-exon list size: 456


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.5    
1.7    
2.0    
2.2    
2.4    
2.6    
2.8    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.0    
5.2    
5.5    
5.7    
5.9    
6.1    
6.3    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.9    
8.1    
8.3    
8.5    
8.7    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
10.9    
11.1    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.1    
15.3    
15.5    
15.7    
15.9    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.5    
17.7    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.2    
19.4    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
21.0    
21.2    
21.4    
21.6    
21.8    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.4    
23.6    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.8    
26.0    
26.2    
26.4    
26.6    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.1    
34.3    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.3    
41.5    
41.7    
41.9    
42.1    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.2    
47.4    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.6    
52.8    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.0    
55.2    
55.5    
55.7    
55.9    
56.1    
56.3    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.9    
58.1    
58.3    
58.5    
58.7    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.3    
63.5    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.7    
65.9    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.5    
67.7    
67.9    
68.1    
68.3    
68.6    
68.8    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.4    
73.6    
73.8    
74.0    
74.2    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.4    
76.6    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.7    
93.9    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.2    
97.4    
97.6    
97.8    
98.0    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 21687, rend_intergenic: 18269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26135, rend_intergenic: 22835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35062, rend_intergenic: 32916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43080, rend_intergenic: 38778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69230, rend_intergenic: 66094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95369, rend_intergenic: 88849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98254, rend_intergenic: 96937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126269, rend_intergenic: 124354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128257, rend_intergenic: 126715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support