-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_15585783-15750103

-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.3002-T1
Valid prediction for GlimmerHMM_glimmerT_8079-T1
Valid prediction for snap_scaffold_3-snap.2986-T1
Valid prediction for GeneMark_model.13164_t
Valid prediction for GeneMark_model.13157_t
Valid prediction for snap_scaffold_3-snap.3008-T1
Valid prediction for snap_scaffold_3-snap.2988-T1
Valid prediction for GeneMark_model.13159_t
Valid prediction for GeneMark_model.13136_t
Valid prediction for GeneMark_model.13137_t
Valid prediction for GeneMark_model.13174_t
Valid prediction for GeneMark_model.13172_t
Valid prediction for GlimmerHMM_glimmerT_8073-T1
Valid prediction for GeneMark_model.13151_t
Valid prediction for GeneMark_model.13142_t
Valid prediction for GeneMark_model.13148_t
Valid prediction for snap_scaffold_3-snap.2985-T1
Valid prediction for GeneMark_model.13152_t
Valid prediction for snap_scaffold_3-snap.2987-T1
Valid prediction for snap_scaffold_3-snap.2991-T1
Valid prediction for GeneMark_model.13140_t
Valid prediction for snap_scaffold_3-snap.3003-T1
Valid prediction for GeneMark_model.13147_t
Valid prediction for GlimmerHMM_glimmerT_8078-T1
Valid prediction for snap_scaffold_3-snap.3004-T1
Valid prediction for Augustus_model.g5364.t1
Valid prediction for snap_scaffold_3-snap.3000-T1
Valid prediction for snap_scaffold_3-snap.2993-T1
Valid prediction for GeneMark_model.13162_t
Valid prediction for GeneMark_model.13156_t
Valid prediction for snap_scaffold_3-snap.2994-T1
Valid prediction for GlimmerHMM_glimmerT_8084-T1
Valid prediction for snap_scaffold_3-snap.2997-T1
Valid prediction for snap_scaffold_3-snap.3010-T1
Valid prediction for GeneMark_model.13168_t
Valid prediction for GlimmerHMM_glimmerT_8072-T1
Valid prediction for GlimmerHMM_glimmerT_8075-T1
Valid prediction for GeneMark_model.13146_t
Valid prediction for snap_scaffold_3-snap.2983-T1
Valid prediction for GlimmerHMM_glimmerT_8080-T1
Valid prediction for GlimmerHMM_glimmerT_8077-T1
Valid prediction for Augustus_model.g5362.t1
Valid prediction for GlimmerHMM_glimmerT_8071-T1
Valid prediction for GeneMark_model.13144_t
Valid prediction for GeneMark_model.13161_t
Valid prediction for GeneMark_model.13166_t
Valid prediction for snap_scaffold_3-snap.2981-T1
Valid prediction for snap_scaffold_3-snap.2989-T1
Valid prediction for snap_scaffold_3-snap.2998-T1
Valid prediction for snap_scaffold_3-snap.3001-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.3009-T1
Valid prediction for GeneMark_model.13165_t
Valid prediction for snap_scaffold_3-snap.3012-T1
Valid prediction for GeneMark_model.13139_t
Valid prediction for snap_scaffold_3-snap.2980-T1
Valid prediction for GeneMark_model.13143_t
Valid prediction for GeneMark_model.13150_t
Valid prediction for CodingQuarry_transcript_46282-T1
Valid prediction for CodingQuarry_transcript_46283-T1
Valid prediction for GlimmerHMM_glimmerT_8088-T1
Valid prediction for GeneMark_model.13155_t
Valid prediction for GeneMark_model.13176_t
Valid prediction for GeneMark_model.13141_t
Valid prediction for GeneMark_model.13167_t
Valid prediction for GlimmerHMM_glimmerT_8085-T1
Valid prediction for GeneMark_model.13173_t
Valid prediction for snap_scaffold_3-snap.2996-T1
Valid prediction for snap_scaffold_3-snap.3007-T1
Valid prediction for GeneMark_model.13138_t
Valid prediction for GeneMark_model.13154_t
Valid prediction for snap_scaffold_3-snap.3011-T1
Valid prediction for snap_scaffold_3-snap.2984-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.13175_t
Valid prediction for GlimmerHMM_glimmerT_8076-T1
Valid prediction for pasa_asmbl_39387.p1
Valid prediction for GeneMark_model.13153_t
Valid prediction for GeneMark_model.13170_t
Valid prediction for GlimmerHMM_glimmerT_8087-T1
Valid prediction for GeneMark_model.13163_t
Valid prediction for GeneMark_model.13171_t
Couldn't classify 77076, 77208
Couldn't classify 83848, 83871
Sorry, prediction pasa_asmbl_39385.p1 fails validation.
(CTC)	 AG	77076-77208	GT	AGG
(GGA)	 AG	78564-78772	GT	AGG
(GTT)	 AG	81313-81370	GT	AGG
(GTG)	 AG	81660-81748	GT	AGG
(GTA)	 AG	83848-83871	GG	AAG
-recovered pasa_asmbl_39385.p1, internal, 77076, 77208
-recovered pasa_asmbl_39385.p1, internal, 78564, 78772
-recovered pasa_asmbl_39385.p1, internal, 81313, 81370
-recovered pasa_asmbl_39385.p1, internal, 81660, 81748
Valid prediction for HiQ_model.g5363.t1
Valid prediction for GeneMark_model.13145_t
Valid prediction for snap_scaffold_3-snap.2990-T1
Valid prediction for GeneMark_model.13158_t
Valid prediction for snap_scaffold_3-snap.2999-T1
Valid prediction for GlimmerHMM_glimmerT_8074-T1
Valid prediction for GlimmerHMM_glimmerT_8082-T1
Valid prediction for HiQ_model.g5366.t1
Valid prediction for GeneMark_model.13160_t
Valid prediction for Augustus_model.g5365.t1
Valid prediction for snap_scaffold_3-snap.2982-T1
Valid prediction for GlimmerHMM_glimmerT_8081-T1
Valid prediction for Augustus_model.g5361.t1
Valid prediction for snap_scaffold_3-snap.3005-T1
Valid prediction for GlimmerHMM_glimmerT_8086-T1
Valid prediction for GeneMark_model.13149_t
Valid prediction for snap_scaffold_3-snap.2995-T1
Valid prediction for snap_scaffold_3-snap.3006-T1
Valid prediction for snap_scaffold_3-snap.2992-T1
Valid prediction for GlimmerHMM_glimmerT_8083-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6658, rend_intergenic: 1730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10040, rend_intergenic: 6885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18122, rend_intergenic: 14148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99209, rend_intergenic: 97858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109899, rend_intergenic: 99837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128237, rend_intergenic: 124437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132400, rend_intergenic: 131384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146277, rend_intergenic: 140057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164321
-exon list size: 384


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.4    
3.6    
3.9    
4.1    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
6.0    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.0    
8.3    
8.5    
8.8    
9.1    
9.3    
9.6    
9.8    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.1    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.8    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.2    
26.4    
26.7    
26.9    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.9    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.1    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.5    
72.8    
73.1    
73.3    
73.6    
73.8    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.2    
76.4    
76.7    
76.9    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.9    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
90.9    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 6658, rend_intergenic: 1730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10040, rend_intergenic: 6885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18122, rend_intergenic: 14148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99209, rend_intergenic: 97858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109899, rend_intergenic: 99837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128237, rend_intergenic: 124437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132400, rend_intergenic: 131384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146277, rend_intergenic: 140057  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