-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_756853-1017959

-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 Augustus_model.g23734.t1
Valid prediction for HiQ_model.g23724.t1
Valid prediction for snap_scaffold_15-snap.215-T1
Valid prediction for Augustus_model.g23733.t1
Valid prediction for snap_scaffold_15-snap.197-T1
Valid prediction for snap_scaffold_15-snap.199-T1
Valid prediction for snap_scaffold_15-snap.200-T1
Valid prediction for Augustus_model.g23718.t1
Valid prediction for snap_scaffold_15-snap.188-T1
Valid prediction for snap_scaffold_15-snap.191-T1
Valid prediction for snap_scaffold_15-snap.213-T1
Valid prediction for snap_scaffold_15-snap.226-T1
Valid prediction for GlimmerHMM_glimmerT_35547-T1
Couldn't classify 189864, 189917
Sorry, prediction pasa_asmbl_14989.p1 fails validation.
(TGG)	 AC	189864-189917	GT	CGG
(GTG)	 AG	192864-193037	GT	AGG
(GAC)	 AG	195366-195534	GT	AGG
(ACC)	 AG	195875-195987	GA	AAG
-recovered pasa_asmbl_14989.p1, terminal, 195875, 195987
-recovered pasa_asmbl_14989.p1, internal, 192864, 193037
-recovered pasa_asmbl_14989.p1, internal, 195366, 195534
Valid prediction for snap_scaffold_15-snap.180-T1
Valid prediction for snap_scaffold_15-snap.187-T1
Valid prediction for snap_scaffold_15-snap.221-T1
Valid prediction for snap_scaffold_15-snap.204-T1
Valid prediction for GlimmerHMM_glimmerT_35560-T1
Valid prediction for snap_scaffold_15-snap.209-T1
Valid prediction for GlimmerHMM_glimmerT_35549-T1
Valid prediction for snap_scaffold_15-snap.194-T1
Valid prediction for snap_scaffold_15-snap.205-T1
Valid prediction for Augustus_model.g23731.t1
Valid prediction for Augustus_model.g23732.t1
Valid prediction for snap_scaffold_15-snap.222-T1
Valid prediction for Augustus_model.g23727.t1
Valid prediction for GlimmerHMM_glimmerT_35548-T1
Valid prediction for GlimmerHMM_glimmerT_35539-T1
Valid prediction for snap_scaffold_15-snap.198-T1
Valid prediction for Augustus_model.g23719.t1
Valid prediction for snap_scaffold_15-snap.201-T1
Couldn't classify 199401, 199678
Couldn't classify 202222, 202474
Sorry, prediction pasa_asmbl_14992.p1 fails validation.
(TAC)	 TG	199401-199678	GT	TGG
(GTT)	 AG	202222-202474	GG	AGG
Valid prediction for snap_scaffold_15-snap.202-T1
Couldn't classify 207518, 207696
Sorry, prediction pasa_asmbl_14993.p1 fails validation.
(TCC)	 AT	207518-207696	GT	TGG
(GTA)	 AG	208249-209995	TC	GAT
-recovered pasa_asmbl_14993.p1, terminal, 208249, 209995
Valid prediction for pasa_asmbl_14988.p1
Valid prediction for GlimmerHMM_glimmerT_35542-T1
Valid prediction for snap_scaffold_15-snap.186-T1
Valid prediction for snap_scaffold_15-snap.219-T1
Valid prediction for GlimmerHMM_glimmerT_35555-T1
Valid prediction for Augustus_model.g23735.t1
Valid prediction for GlimmerHMM_glimmerT_35544-T1
Valid prediction for snap_scaffold_15-snap.196-T1
Valid prediction for GlimmerHMM_glimmerT_35546-T1
Valid prediction for snap_scaffold_15-snap.189-T1
Valid prediction for Augustus_model.g23720.t1
Valid prediction for GlimmerHMM_glimmerT_35557-T1
Valid prediction for Augustus_model.g23721.t1
Valid prediction for snap_scaffold_15-snap.183-T1
Valid prediction for GlimmerHMM_glimmerT_35554-T1
Valid prediction for snap_scaffold_15-snap.211-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35541-T1
Valid prediction for snap_scaffold_15-snap.217-T1
Valid prediction for CodingQuarry_transcript_17897-T1
Valid prediction for Augustus_model.g23722.t1
Valid prediction for snap_scaffold_15-snap.210-T1
Valid prediction for snap_scaffold_15-snap.218-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 pasa_asmbl_14863.p1
Valid prediction for snap_scaffold_15-snap.214-T1
Valid prediction for snap_scaffold_15-snap.193-T1
Valid prediction for Augustus_model.g23728.t1
Valid prediction for GlimmerHMM_glimmerT_35552-T1
Valid prediction for GlimmerHMM_glimmerT_35540-T1
Valid prediction for Augustus_model.g23723.t1
Valid prediction for GlimmerHMM_glimmerT_35545-T1
Valid prediction for CodingQuarry_transcript_17898-T1
Valid prediction for GlimmerHMM_glimmerT_35559-T1
Valid prediction for GlimmerHMM_glimmerT_35551-T1
Valid prediction for CodingQuarry_transcript_17900-T1
Valid prediction for GlimmerHMM_glimmerT_35550-T1
Valid prediction for HiQ_model.g23726.t1
Valid prediction for snap_scaffold_15-snap.190-T1
Valid prediction for snap_scaffold_15-snap.207-T1
Valid prediction for snap_scaffold_15-snap.184-T1
Valid prediction for snap_scaffold_15-snap.225-T1
Valid prediction for snap_scaffold_15-snap.203-T1
Valid prediction for snap_scaffold_15-snap.208-T1
Valid prediction for GlimmerHMM_glimmerT_35553-T1
Valid prediction for snap_scaffold_15-snap.195-T1
Valid prediction for Augustus_model.g23729.t1
Valid prediction for GlimmerHMM_glimmerT_35556-T1
Valid prediction for snap_scaffold_15-snap.212-T1
Valid prediction for Augustus_model.g23730.t1
Valid prediction for snap_scaffold_15-snap.185-T1
Valid prediction for snap_scaffold_15-snap.216-T1
Valid prediction for snap_scaffold_15-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_35543-T1
Valid prediction for GlimmerHMM_glimmerT_35537-T1
Valid prediction for snap_scaffold_15-snap.223-T1
Valid prediction for snap_scaffold_15-snap.224-T1
Valid prediction for snap_scaffold_15-snap.182-T1
Valid prediction for snap_scaffold_15-snap.192-T1
Valid prediction for HiQ_model.g23725.t1
Valid prediction for GlimmerHMM_glimmerT_35538-T1
Valid prediction for snap_scaffold_15-snap.181-T1
Valid prediction for HiQ_model.g23736.t1
Valid prediction for GlimmerHMM_glimmerT_35558-T1
Valid prediction for pasa_asmbl_13946.p1
Valid prediction for snap_scaffold_15-snap.206-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4447, rend_intergenic: 3459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12213, rend_intergenic: 10395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71983, rend_intergenic: 70819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74086, rend_intergenic: 72589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188513, rend_intergenic: 181899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201074, rend_intergenic: 199260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209995, rend_intergenic: 207554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223694, rend_intergenic: 221859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 261107
-exon list size: 319


building trellis

0.3    
0.6    
0.9    
1.2    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.8    
99.1    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 4447, rend_intergenic: 3459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12213, rend_intergenic: 10395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71983, rend_intergenic: 70819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74086, rend_intergenic: 72589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188513, rend_intergenic: 181899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201074, rend_intergenic: 199260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209995, rend_intergenic: 207554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223694, rend_intergenic: 221859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support