-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_4171273-4315867

-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 GeneMark_model.96520_t
Valid prediction for GeneMark_model.96544_t
Valid prediction for GeneMark_model.96535_t
Valid prediction for snap_scaffold_25-snap.894-T1
Valid prediction for snap_scaffold_25-snap.895-T1
Valid prediction for Augustus_model.g36882.t1
Valid prediction for snap_scaffold_25-snap.892-T1
Valid prediction for GlimmerHMM_glimmerT_55279-T1
Valid prediction for snap_scaffold_25-snap.899-T1
Valid prediction for snap_scaffold_25-snap.908-T1
Valid prediction for GlimmerHMM_glimmerT_55266-T1
Valid prediction for snap_scaffold_25-snap.911-T1
Valid prediction for GlimmerHMM_glimmerT_55281-T1
Valid prediction for GlimmerHMM_glimmerT_55282-T1
Valid prediction for Augustus_model.g36878.t1
Valid prediction for Augustus_model.g36873.t1
Valid prediction for GeneMark_model.96523_t
Valid prediction for GlimmerHMM_glimmerT_55288-T1
Valid prediction for GeneMark_model.96539_t
Valid prediction for GeneMark_model.96533_t
Valid prediction for GeneMark_model.96543_t
Valid prediction for Augustus_model.g36883.t1
Valid prediction for GeneMark_model.96529_t
Valid prediction for Augustus_model.g36874.t1
Valid prediction for Augustus_model.g36880.t1
Valid prediction for GlimmerHMM_glimmerT_55289-T1
Couldn't classify 52219, 52281
Sorry, prediction pasa_asmbl_33478.p1 fails validation.
(CTT)	 GG	52219-52281	GT	CGG
(TTT)	 AG	53180-53385	GT	AAG
(ACA)	 AG	53683-53716	CT	AGC
-recovered pasa_asmbl_33478.p1, terminal, 53683, 53716
-recovered pasa_asmbl_33478.p1, internal, 53180, 53385
Valid prediction for GeneMark_model.96512_t
Valid prediction for GeneMark_model.96516_t
Valid prediction for Augustus_model.g36875.t1
Valid prediction for snap_scaffold_25-snap.903-T1
Valid prediction for GlimmerHMM_glimmerT_55284-T1
Valid prediction for snap_scaffold_25-snap.888-T1
Valid prediction for snap_scaffold_25-snap.897-T1
Valid prediction for GeneMark_model.96525_t
Valid prediction for snap_scaffold_25-snap.883-T1
Valid prediction for GeneMark_model.96541_t
Valid prediction for GeneMark_model.96527_t
Valid prediction for snap_scaffold_25-snap.906-T1
Valid prediction for GlimmerHMM_glimmerT_55267-T1
Valid prediction for GeneMark_model.96530_t
Valid prediction for GlimmerHMM_glimmerT_55271-T1
Valid prediction for GeneMark_model.96538_t
Valid prediction for GeneMark_model.96514_t
Valid prediction for Augustus_model.g36871.t1
Valid prediction for GlimmerHMM_glimmerT_55287-T1
Valid prediction for snap_scaffold_25-snap.905-T1
Valid prediction for GlimmerHMM_glimmerT_55277-T1
Valid prediction for GlimmerHMM_glimmerT_55268-T1
Valid prediction for GlimmerHMM_glimmerT_55270-T1
Valid prediction for GeneMark_model.96515_t
Valid prediction for snap_scaffold_25-snap.900-T1
Valid prediction for Augustus_model.g36870.t1
Valid prediction for snap_scaffold_25-snap.896-T1
Valid prediction for GlimmerHMM_glimmerT_55275-T1
Valid prediction for GlimmerHMM_glimmerT_55274-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_25-snap.909-T1
Valid prediction for Augustus_model.g36872.t1
Valid prediction for Augustus_model.g36876.t1
Valid prediction for GlimmerHMM_glimmerT_55285-T1
Valid prediction for GeneMark_model.96526_t
Valid prediction for snap_scaffold_25-snap.893-T1
Valid prediction for GlimmerHMM_glimmerT_55286-T1
Valid prediction for GeneMark_model.96521_t
Valid prediction for snap_scaffold_25-snap.912-T1
Valid prediction for GeneMark_model.96532_t
Valid prediction for snap_scaffold_25-snap.889-T1
Valid prediction for Augustus_model.g36881.t1
Valid prediction for snap_scaffold_25-snap.885-T1
Valid prediction for GeneMark_model.96528_t
Valid prediction for Augustus_model.g36877.t1
Valid prediction for GeneMark_model.96540_t
Valid prediction for snap_scaffold_25-snap.910-T1
Valid prediction for snap_scaffold_25-snap.884-T1
Valid prediction for snap_scaffold_25-snap.891-T1
Valid prediction for CodingQuarry_transcript_38609-T1
Valid prediction for snap_scaffold_25-snap.898-T1
Valid prediction for GeneMark_model.96531_t
Valid prediction for GeneMark_model.96519_t
Valid prediction for snap_scaffold_25-snap.902-T1
Valid prediction for snap_scaffold_25-snap.890-T1
Valid prediction for snap_scaffold_25-snap.887-T1
Valid prediction for GlimmerHMM_glimmerT_55273-T1
Valid prediction for GeneMark_model.96536_t
Valid prediction for GeneMark_model.96522_t
Valid prediction for GeneMark_model.96545_t
Valid prediction for GeneMark_model.96542_t
Valid prediction for GlimmerHMM_glimmerT_55280-T1
Valid prediction for Augustus_model.g36879.t1
Valid prediction for GeneMark_model.96537_t
Valid prediction for snap_scaffold_25-snap.913-T1
Valid prediction for snap_scaffold_25-snap.901-T1
Valid prediction for snap_scaffold_25-snap.907-T1
Valid prediction for GeneMark_model.96518_t
Valid prediction for GeneMark_model.96534_t
Valid prediction for GeneMark_model.96524_t
Valid prediction for GlimmerHMM_glimmerT_55269-T1
Valid prediction for snap_scaffold_25-snap.904-T1
Valid prediction for GeneMark_model.96513_t
Valid prediction for GeneMark_model.96511_t
Valid prediction for GlimmerHMM_glimmerT_55276-T1
Valid prediction for GlimmerHMM_glimmerT_55272-T1
Valid prediction for GlimmerHMM_glimmerT_55283-T1
Valid prediction for snap_scaffold_25-snap.886-T1
Valid prediction for GlimmerHMM_glimmerT_55278-T1
Valid prediction for GeneMark_model.96517_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 96121, rend_intergenic: 93379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117042, rend_intergenic: 115304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 71592, rend_intergenic: 71589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 144595
-exon list size: 417


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.9    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.5    
4.8    
5.0    
5.3    
5.5    
5.7    
6.0    
6.2    
6.4    
6.7    
6.9    
7.2    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.8    
9.1    
9.3    
9.5    
9.8    
10.0    
10.3    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
11.9    
12.2    
12.4    
12.6    
12.9    
13.1    
13.4    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.2    
16.5    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.8    
21.0    
21.2    
21.5    
21.7    
22.0    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.8    
30.1    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.1    
55.4    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.0    
57.3    
57.5    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.5    
62.8    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.4    
64.7    
64.9    
65.2    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
69.9    
70.2    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 96121, rend_intergenic: 93379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117042, rend_intergenic: 115304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 71592, rend_intergenic: 71589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support