-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_15208900-15374638

-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.2929-T1
Valid prediction for snap_scaffold_3-snap.2898-T1
Valid prediction for snap_scaffold_3-snap.2906-T1
Valid prediction for snap_scaffold_3-snap.2891-T1
Valid prediction for GlimmerHMM_glimmerT_7857-T1
Valid prediction for GlimmerHMM_glimmerT_7858-T1
Valid prediction for Augustus_model.g5186.t1
Valid prediction for GlimmerHMM_glimmerT_7863-T1
Valid prediction for snap_scaffold_3-snap.2900-T1
Valid prediction for snap_scaffold_3-snap.2925-T1
Valid prediction for snap_scaffold_3-snap.2916-T1
Valid prediction for snap_scaffold_3-snap.2904-T1
Valid prediction for snap_scaffold_3-snap.2931-T1
Valid prediction for snap_scaffold_3-snap.2902-T1
Valid prediction for snap_scaffold_3-snap.2914-T1
Valid prediction for snap_scaffold_3-snap.2910-T1
Valid prediction for Augustus_model.g5180.t1
Valid prediction for snap_scaffold_3-snap.2918-T1
Valid prediction for Augustus_model.g5185.t1
Valid prediction for snap_scaffold_3-snap.2887-T1
Valid prediction for snap_scaffold_3-snap.2915-T1
Valid prediction for snap_scaffold_3-snap.2912-T1
Valid prediction for snap_scaffold_3-snap.2920-T1
Valid prediction for GlimmerHMM_glimmerT_7847-T1
Valid prediction for GlimmerHMM_glimmerT_7854-T1
Valid prediction for snap_scaffold_3-snap.2922-T1
Valid prediction for snap_scaffold_3-snap.2917-T1
Valid prediction for GlimmerHMM_glimmerT_7851-T1
Valid prediction for GlimmerHMM_glimmerT_7849-T1
Valid prediction for snap_scaffold_3-snap.2896-T1
Valid prediction for GlimmerHMM_glimmerT_7859-T1
Valid prediction for GlimmerHMM_glimmerT_7852-T1
Valid prediction for GlimmerHMM_glimmerT_7856-T1
Valid prediction for snap_scaffold_3-snap.2909-T1
Valid prediction for snap_scaffold_3-snap.2893-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.2928-T1
Valid prediction for GlimmerHMM_glimmerT_7841-T1
Valid prediction for GlimmerHMM_glimmerT_7862-T1
Valid prediction for Augustus_model.g5182.t1
Valid prediction for snap_scaffold_3-snap.2897-T1
Valid prediction for snap_scaffold_3-snap.2908-T1
Valid prediction for snap_scaffold_3-snap.2899-T1
Valid prediction for snap_scaffold_3-snap.2919-T1
Valid prediction for GlimmerHMM_glimmerT_7865-T1
Valid prediction for GlimmerHMM_glimmerT_7842-T1
Valid prediction for snap_scaffold_3-snap.2889-T1
Valid prediction for snap_scaffold_3-snap.2921-T1
Valid prediction for snap_scaffold_3-snap.2907-T1
Valid prediction for Augustus_model.g5192.t1
Valid prediction for snap_scaffold_3-snap.2901-T1
Valid prediction for GlimmerHMM_glimmerT_7866-T1
Valid prediction for GlimmerHMM_glimmerT_7860-T1
Valid prediction for GlimmerHMM_glimmerT_7861-T1
Valid prediction for snap_scaffold_3-snap.2913-T1
Valid prediction for GlimmerHMM_glimmerT_7853-T1
Valid prediction for GlimmerHMM_glimmerT_7850-T1
Valid prediction for Augustus_model.g5188.t1
Valid prediction for GlimmerHMM_glimmerT_7855-T1
Valid prediction for snap_scaffold_3-snap.2924-T1
Valid prediction for snap_scaffold_3-snap.2905-T1
Valid prediction for snap_scaffold_3-snap.2895-T1
Valid prediction for GlimmerHMM_glimmerT_7846-T1
Valid prediction for GlimmerHMM_glimmerT_7864-T1
Valid prediction for GlimmerHMM_glimmerT_7868-T1
Valid prediction for GlimmerHMM_glimmerT_7867-T1
Valid prediction for Augustus_model.g5189.t1
Valid prediction for snap_scaffold_3-snap.2894-T1
Valid prediction for Augustus_model.g5184.t1
Valid prediction for snap_scaffold_3-snap.2903-T1
Valid prediction for snap_scaffold_3-snap.2888-T1
Valid prediction for snap_scaffold_3-snap.2926-T1
Valid prediction for Augustus_model.g5187.t1
Valid prediction for Augustus_model.g5183.t1
Valid prediction for snap_scaffold_3-snap.2890-T1
Valid prediction for Augustus_model.g5194.t1
Valid prediction for Augustus_model.g5181.t1
Valid prediction for GlimmerHMM_glimmerT_7843-T1
Couldn't classify 56512, 56571
Sorry, prediction pasa_asmbl_39791.p1 fails validation.
(ATG)	 TG	52508-52657	GT	GGG
(GGG)	 AG	53305-53436	GT	AGG
(GTC)	 AG	53577-53656	GT	AGG
(GCT)	 AG	55271-55378	GT	CAG
(ACC)	 AG	55599-55740	GT	TGG
(TAT)	 AG	56512-56571	AA	TCA
-recovered pasa_asmbl_39791.p1, initial, 52508, 52657
-recovered pasa_asmbl_39791.p1, internal, 53305, 53436
-recovered pasa_asmbl_39791.p1, internal, 53577, 53656
-recovered pasa_asmbl_39791.p1, internal, 55271, 55378
-recovered pasa_asmbl_39791.p1, internal, 55599, 55740
Valid prediction for GlimmerHMM_glimmerT_7844-T1
Couldn't classify 48236, 48389
Sorry, prediction pasa_asmbl_39433.p1 fails validation.
(ATG)	 CC	46534-46695	GT	AGG
(GAC)	 AG	47913-48028	GT	AGG
(GCT)	 AG	48236-48389	GC	AGG
-recovered pasa_asmbl_39433.p1, initial, 46534, 46695
-recovered pasa_asmbl_39433.p1, internal, 47913, 48028
-recovered pasa_asmbl_39433.p1, internal, 48236, 48389
Valid prediction for Augustus_model.g5190.t1
Valid prediction for GlimmerHMM_glimmerT_7845-T1
Valid prediction for GlimmerHMM_glimmerT_7848-T1
Valid prediction for snap_scaffold_3-snap.2923-T1
Valid prediction for Augustus_model.g5193.t1
Valid prediction for snap_scaffold_3-snap.2927-T1
Valid prediction for snap_scaffold_3-snap.2892-T1
Valid prediction for Augustus_model.g5191.t1
Valid prediction for snap_scaffold_3-snap.2911-T1
Couldn't classify 57014, 57059
Sorry, prediction pasa_asmbl_39737.p1 fails validation.
(CAC)	 CA	57014-57059	GT	AGG
(GCA)	 AG	58710-58822	GT	AGG
(GAG)	 AG	59633-59702	GT	AGG
(CGG)	 AG	59987-60135	CC	GAC
-recovered pasa_asmbl_39737.p1, terminal, 59633, 59702
-recovered pasa_asmbl_39737.p1, terminal, 59987, 60135
-recovered pasa_asmbl_39737.p1, internal, 58710, 58822
-recovered pasa_asmbl_39737.p1, internal, 59633, 59702

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20873, rend_intergenic: 18495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29376, rend_intergenic: 21426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32177, rend_intergenic: 29474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38295, rend_intergenic: 35429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41625, rend_intergenic: 38773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49847, rend_intergenic: 45774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53995, rend_intergenic: 49920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60034, rend_intergenic: 58488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62978, rend_intergenic: 61173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65215, rend_intergenic: 64594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67782, rend_intergenic: 66343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69958, rend_intergenic: 68788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85677, rend_intergenic: 83260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90520, rend_intergenic: 88676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94972, rend_intergenic: 91840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110639, rend_intergenic: 105605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129946, rend_intergenic: 127657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148004, rend_intergenic: 141876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154693, rend_intergenic: 153825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165739
-exon list size: 317


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
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    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 20873, rend_intergenic: 18495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29376, rend_intergenic: 21426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32177, rend_intergenic: 29474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38295, rend_intergenic: 35429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41625, rend_intergenic: 38773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49847, rend_intergenic: 45774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53995, rend_intergenic: 49920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60034, rend_intergenic: 58488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62978, rend_intergenic: 61173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65215, rend_intergenic: 64594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67782, rend_intergenic: 66343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69958, rend_intergenic: 68788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85677, rend_intergenic: 83260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90520, rend_intergenic: 88676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94972, rend_intergenic: 91840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110639, rend_intergenic: 105605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129946, rend_intergenic: 127657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148004, rend_intergenic: 141876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154693, rend_intergenic: 153825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support