-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_15041730-15210808

-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 GlimmerHMM_glimmerT_7834-T1
Valid prediction for GlimmerHMM_glimmerT_7833-T1
Valid prediction for snap_scaffold_3-snap.2883-T1
Valid prediction for snap_scaffold_3-snap.2854-T1
Valid prediction for snap_scaffold_3-snap.2874-T1
Valid prediction for Augustus_model.g5165.t1
Valid prediction for GlimmerHMM_glimmerT_7819-T1
Valid prediction for snap_scaffold_3-snap.2868-T1
Valid prediction for GlimmerHMM_glimmerT_7830-T1
Valid prediction for snap_scaffold_3-snap.2860-T1
Couldn't classify 118008, 118109
Couldn't classify 119577, 119743
Sorry, prediction pasa_asmbl_40853.p1 fails validation.
(TTT)	 AG	118008-118109	GT	AGG
(GAC)	 AG	119030-119123	GT	AGG
(GTG)	 AG	119577-119743	GG	CAG
-recovered pasa_asmbl_40853.p1, terminal, 119030, 119123
-recovered pasa_asmbl_40853.p1, internal, 118008, 118109
-recovered pasa_asmbl_40853.p1, internal, 119030, 119123
Valid prediction for snap_scaffold_3-snap.2884-T1
Valid prediction for Augustus_model.g5158.t1
Valid prediction for snap_scaffold_3-snap.2872-T1
Valid prediction for snap_scaffold_3-snap.2863-T1
Valid prediction for GlimmerHMM_glimmerT_7838-T1
Valid prediction for snap_scaffold_3-snap.2870-T1
Valid prediction for snap_scaffold_3-snap.2882-T1
Valid prediction for GlimmerHMM_glimmerT_7827-T1
Valid prediction for Augustus_model.g5173.t1
Valid prediction for GlimmerHMM_glimmerT_7831-T1
Valid prediction for GlimmerHMM_glimmerT_7826-T1
Valid prediction for snap_scaffold_3-snap.2866-T1
Valid prediction for snap_scaffold_3-snap.2855-T1
Valid prediction for Augustus_model.g5164.t1
Valid prediction for snap_scaffold_3-snap.2856-T1
Valid prediction for snap_scaffold_3-snap.2885-T1
Valid prediction for snap_scaffold_3-snap.2878-T1
Valid prediction for GlimmerHMM_glimmerT_7811-T1
Valid prediction for snap_scaffold_3-snap.2879-T1
Valid prediction for snap_scaffold_3-snap.2853-T1
Valid prediction for GlimmerHMM_glimmerT_7822-T1
Valid prediction for Augustus_model.g5163.t1
Valid prediction for Augustus_model.g5167.t1
Valid prediction for Augustus_model.g5178.t1
Valid prediction for GlimmerHMM_glimmerT_7839-T1
Valid prediction for Augustus_model.g5172.t1
Valid prediction for GlimmerHMM_glimmerT_7828-T1
Valid prediction for snap_scaffold_3-snap.2877-T1
Valid prediction for GlimmerHMM_glimmerT_7817-T1
Valid prediction for GlimmerHMM_glimmerT_7820-T1
Valid prediction for GlimmerHMM_glimmerT_7840-T1
Valid prediction for Augustus_model.g5169.t1
Couldn't classify 6844, 6990
Couldn't classify 12352, 12419
Sorry, prediction pasa_asmbl_40561.p1 fails validation.
(GAA)	 TA	6844-6990	GT	AGG
(GGC)	 AG	9208-9355	GT	AGG
(CCA)	 AG	11419-11562	GT	TGG
(ACT)	 AG	12352-12419	GG	AAG
-recovered pasa_asmbl_40561.p1, internal, 9208, 9355
-recovered pasa_asmbl_40561.p1, internal, 11419, 11562
Valid prediction for Augustus_model.g5170.t1
Valid prediction for Augustus_model.g5177.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.2881-T1
Valid prediction for GlimmerHMM_glimmerT_7814-T1
Valid prediction for snap_scaffold_3-snap.2864-T1
Valid prediction for snap_scaffold_3-snap.2857-T1
Valid prediction for GlimmerHMM_glimmerT_7837-T1
Valid prediction for Augustus_model.g5179.t1
Valid prediction for Augustus_model.g5161.t1
Valid prediction for Augustus_model.g5176.t1
Valid prediction for snap_scaffold_3-snap.2858-T1
Valid prediction for Augustus_model.g5162.t1
Valid prediction for GlimmerHMM_glimmerT_7823-T1
Valid prediction for GlimmerHMM_glimmerT_7815-T1
Valid prediction for Augustus_model.g5175.t1
Valid prediction for snap_scaffold_3-snap.2859-T1
Valid prediction for GlimmerHMM_glimmerT_7816-T1
Valid prediction for snap_scaffold_3-snap.2851-T1
Valid prediction for GlimmerHMM_glimmerT_7821-T1
Valid prediction for GlimmerHMM_glimmerT_7835-T1
Valid prediction for GlimmerHMM_glimmerT_7829-T1
Valid prediction for snap_scaffold_3-snap.2852-T1
Valid prediction for Augustus_model.g5159.t1
Valid prediction for Augustus_model.g5166.t1
Valid prediction for snap_scaffold_3-snap.2871-T1
Valid prediction for snap_scaffold_3-snap.2869-T1
Valid prediction for snap_scaffold_3-snap.2873-T1
Valid prediction for snap_scaffold_3-snap.2865-T1
Valid prediction for snap_scaffold_3-snap.2867-T1
Valid prediction for GlimmerHMM_glimmerT_7832-T1
Valid prediction for snap_scaffold_3-snap.2876-T1
Valid prediction for snap_scaffold_3-snap.2880-T1
Valid prediction for GlimmerHMM_glimmerT_7812-T1
Valid prediction for snap_scaffold_3-snap.2862-T1
Valid prediction for snap_scaffold_3-snap.2875-T1
Valid prediction for Augustus_model.g5171.t1
Valid prediction for GlimmerHMM_glimmerT_7824-T1
Valid prediction for snap_scaffold_3-snap.2861-T1
Valid prediction for snap_scaffold_3-snap.2886-T1
Valid prediction for Augustus_model.g5160.t1
Valid prediction for Augustus_model.g5168.t1
Valid prediction for GlimmerHMM_glimmerT_7818-T1
Valid prediction for GlimmerHMM_glimmerT_7825-T1
Valid prediction for GlimmerHMM_glimmerT_7813-T1
Valid prediction for Augustus_model.g5174.t1
Valid prediction for GlimmerHMM_glimmerT_7836-T1
Valid prediction for GlimmerHMM_glimmerT_7810-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6428, rend_intergenic: 5206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77933, rend_intergenic: 74434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82620, rend_intergenic: 78074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84337, rend_intergenic: 83785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86994, rend_intergenic: 84530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108400, rend_intergenic: 91299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110343, rend_intergenic: 108699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125360, rend_intergenic: 112174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 68057, rend_intergenic: 68054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169079
-exon list size: 230


building trellis

0.4    
0.9    
1.3    
1.7    
2.2    
2.6    
3.0    
3.4    
3.9    
4.3    
4.7    
5.2    
5.6    
6.0    
6.5    
6.9    
7.3    
7.8    
8.2    
8.6    
9.1    
9.5    
9.9    
10.3    
10.8    
11.2    
11.6    
12.1    
12.5    
12.9    
13.4    
13.8    
14.2    
14.7    
15.1    
15.5    
15.9    
16.4    
16.8    
17.2    
17.7    
18.1    
18.5    
19.0    
19.4    
19.8    
20.3    
20.7    
21.1    
21.6    
22.0    
22.4    
22.8    
23.3    
23.7    
24.1    
24.6    
25.0    
25.4    
25.9    
26.3    
26.7    
27.2    
27.6    
28.0    
28.4    
28.9    
29.3    
29.7    
30.2    
30.6    
31.0    
31.5    
31.9    
32.3    
32.8    
33.2    
33.6    
34.1    
34.5    
34.9    
35.3    
35.8    
36.2    
36.6    
37.1    
37.5    
37.9    
38.4    
38.8    
39.2    
39.7    
40.1    
40.5    
40.9    
41.4    
41.8    
42.2    
42.7    
43.1    
43.5    
44.0    
44.4    
44.8    
45.3    
45.7    
46.1    
46.6    
47.0    
47.4    
47.8    
48.3    
48.7    
49.1    
49.6    
50.0    
50.4    
50.9    
51.3    
51.7    
52.2    
52.6    
53.0    
53.4    
53.9    
54.3    
54.7    
55.2    
55.6    
56.0    
56.5    
56.9    
57.3    
57.8    
58.2    
58.6    
59.1    
59.5    
59.9    
60.3    
60.8    
61.2    
61.6    
62.1    
62.5    
62.9    
63.4    
63.8    
64.2    
64.7    
65.1    
65.5    
65.9    
66.4    
66.8    
67.2    
67.7    
68.1    
68.5    
69.0    
69.4    
69.8    
70.3    
70.7    
71.1    
71.6    
72.0    
72.4    
72.8    
73.3    
73.7    
74.1    
74.6    
75.0    
75.4    
75.9    
76.3    
76.7    
77.2    
77.6    
78.0    
78.4    
78.9    
79.3    
79.7    
80.2    
80.6    
81.0    
81.5    
81.9    
82.3    
82.8    
83.2    
83.6    
84.1    
84.5    
84.9    
85.3    
85.8    
86.2    
86.6    
87.1    
87.5    
87.9    
88.4    
88.8    
89.2    
89.7    
90.1    
90.5    
90.9    
91.4    
91.8    
92.2    
92.7    
93.1    
93.5    
94.0    
94.4    
94.8    
95.3    
95.7    
96.1    
96.6    
97.0    
97.4    
97.8    
98.3    
98.7    
99.1    
99.6    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 6428, rend_intergenic: 5206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77933, rend_intergenic: 74434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82620, rend_intergenic: 78074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84337, rend_intergenic: 83785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86994, rend_intergenic: 84530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108400, rend_intergenic: 91299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110343, rend_intergenic: 108699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125360, rend_intergenic: 112174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 68057, rend_intergenic: 68054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support