-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_1920340-2120336

-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.10254_t
Valid prediction for snap_scaffold_3-snap.469-T1
Valid prediction for GeneMark_model.10251_t
Valid prediction for GlimmerHMM_glimmerT_6224-T1
Valid prediction for snap_scaffold_3-snap.462-T1
Valid prediction for snap_scaffold_3-snap.466-T1
Valid prediction for snap_scaffold_3-snap.465-T1
Valid prediction for snap_scaffold_3-snap.495-T1
Couldn't classify 28642, 28785
Sorry, prediction pasa_asmbl_40836.p2 fails validation.
(ATG)	 GG	25714-25788	GT	AGG
(TGG)	 AG	26783-26893	GT	TGG
(ACA)	 AG	27100-27195	GT	AGG
(GCA)	 AG	28373-28480	GT	TGG
(GCA)	 AG	28642-28785	GT	AGG
-recovered pasa_asmbl_40836.p2, initial, 25714, 25788
-recovered pasa_asmbl_40836.p2, internal, 26783, 26893
-recovered pasa_asmbl_40836.p2, internal, 27100, 27195
-recovered pasa_asmbl_40836.p2, internal, 28373, 28480
-recovered pasa_asmbl_40836.p2, internal, 28642, 28785
Valid prediction for GlimmerHMM_glimmerT_6241-T1
Valid prediction for GlimmerHMM_glimmerT_6235-T1
Valid prediction for Augustus_model.g4102.t1
Valid prediction for GeneMark_model.10244_t
Valid prediction for snap_scaffold_3-snap.471-T1
Valid prediction for GlimmerHMM_glimmerT_6231-T1
Valid prediction for GeneMark_model.10231_t
Valid prediction for GlimmerHMM_glimmerT_6229-T1
Valid prediction for GlimmerHMM_glimmerT_6237-T1
Valid prediction for GlimmerHMM_glimmerT_6238-T1
Valid prediction for GlimmerHMM_glimmerT_6236-T1
Valid prediction for GeneMark_model.10237_t
Valid prediction for Augustus_model.g4098.t1
Valid prediction for snap_scaffold_3-snap.492-T1
Valid prediction for Augustus_model.g4099.t1
Valid prediction for Augustus_model.g4088.t1
Valid prediction for GeneMark_model.10255_t
Valid prediction for snap_scaffold_3-snap.490-T1
Valid prediction for GlimmerHMM_glimmerT_6230-T1
Valid prediction for snap_scaffold_3-snap.481-T1
Valid prediction for Augustus_model.g4092.t1
Valid prediction for snap_scaffold_3-snap.489-T1
Valid prediction for Augustus_model.g4096.t1
Valid prediction for GlimmerHMM_glimmerT_6233-T1
Valid prediction for snap_scaffold_3-snap.486-T1
Valid prediction for GeneMark_model.10230_t
Valid prediction for GeneMark_model.10235_t
Valid prediction for GlimmerHMM_glimmerT_6228-T1
Valid prediction for GlimmerHMM_glimmerT_6245-T1
Valid prediction for GeneMark_model.10240_t
Valid prediction for Augustus_model.g4091.t1
Valid prediction for GlimmerHMM_glimmerT_6227-T1
Valid prediction for GlimmerHMM_glimmerT_6247-T1
Valid prediction for GeneMark_model.10246_t
Valid prediction for GlimmerHMM_glimmerT_6243-T1
Valid prediction for snap_scaffold_3-snap.477-T1
Valid prediction for GeneMark_model.10227_t
Valid prediction for snap_scaffold_3-snap.480-T1
Valid prediction for Augustus_model.g4093.t1
Valid prediction for Augustus_model.g4101.t1
Valid prediction for GeneMark_model.10238_t
Couldn't classify 31187, 31279
Couldn't classify 32248, 32331
Sorry, prediction pasa_asmbl_40837.p1 fails validation.
(TTT)	 AG	31187-31279	GT	AGG
(AAC)	 AG	31723-31848	GT	AGG
(CCT)	 AG	32248-32331	GT	CCG
-recovered pasa_asmbl_40837.p1, internal, 31187, 31279
-recovered pasa_asmbl_40837.p1, internal, 31723, 31848
-recovered pasa_asmbl_40837.p1, internal, 32248, 32331
Valid prediction for Augustus_model.g4104.t1
Valid prediction for GeneMark_model.10253_t
Valid prediction for snap_scaffold_3-snap.478-T1
Valid prediction for GeneMark_model.10256_t
Valid prediction for GeneMark_model.10241_t
Valid prediction for snap_scaffold_3-snap.494-T1
Valid prediction for snap_scaffold_3-snap.488-T1
Valid prediction for snap_scaffold_3-snap.474-T1
Valid prediction for snap_scaffold_3-snap.468-T1
Valid prediction for snap_scaffold_3-snap.467-T1
Valid prediction for snap_scaffold_3-snap.485-T1
Valid prediction for GeneMark_model.10233_t
Valid prediction for snap_scaffold_3-snap.484-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.482-T1
Valid prediction for GeneMark_model.10248_t
Valid prediction for snap_scaffold_3-snap.487-T1
Valid prediction for GlimmerHMM_glimmerT_6239-T1
Valid prediction for snap_scaffold_3-snap.493-T1
Valid prediction for snap_scaffold_3-snap.491-T1
Valid prediction for Augustus_model.g4095.t1
Valid prediction for GlimmerHMM_glimmerT_6246-T1
Valid prediction for GeneMark_model.10257_t
Valid prediction for GeneMark_model.10252_t
Valid prediction for GeneMark_model.10260_t
Valid prediction for GeneMark_model.10258_t
Valid prediction for snap_scaffold_3-snap.472-T1
Valid prediction for Augustus_model.g4089.t1
Valid prediction for Augustus_model.g4097.t1
Valid prediction for Augustus_model.g4100.t1
Valid prediction for GeneMark_model.10243_t
Valid prediction for GlimmerHMM_glimmerT_6225-T1
Valid prediction for snap_scaffold_3-snap.483-T1
Valid prediction for snap_scaffold_3-snap.473-T1
Valid prediction for snap_scaffold_3-snap.496-T1
Valid prediction for GeneMark_model.10242_t
Valid prediction for GeneMark_model.10239_t
Valid prediction for GlimmerHMM_glimmerT_6240-T1
Valid prediction for GeneMark_model.10228_t
Valid prediction for snap_scaffold_3-snap.464-T1
Valid prediction for GlimmerHMM_glimmerT_6232-T1
Valid prediction for GeneMark_model.10245_t
Valid prediction for GeneMark_model.10229_t
Valid prediction for snap_scaffold_3-snap.463-T1
Valid prediction for GlimmerHMM_glimmerT_6226-T1
Valid prediction for GlimmerHMM_glimmerT_6234-T1
Valid prediction for GeneMark_model.10250_t
Valid prediction for GlimmerHMM_glimmerT_6242-T1
Valid prediction for GeneMark_model.10247_t
Valid prediction for snap_scaffold_3-snap.479-T1
Valid prediction for snap_scaffold_3-snap.476-T1
Valid prediction for Augustus_model.g4105.t1
Valid prediction for GeneMark_model.10232_t
Valid prediction for Augustus_model.g4094.t1
Valid prediction for GlimmerHMM_glimmerT_6244-T1
Valid prediction for Augustus_model.g4090.t1
Valid prediction for snap_scaffold_3-snap.475-T1
Valid prediction for GeneMark_model.10226_t
Valid prediction for GeneMark_model.10236_t
Valid prediction for Augustus_model.g4103.t1
Valid prediction for GeneMark_model.10234_t
Valid prediction for GeneMark_model.10249_t
Valid prediction for snap_scaffold_3-snap.470-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 79738, rend_intergenic: 75874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82507, rend_intergenic: 81334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95121, rend_intergenic: 91501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101762, rend_intergenic: 95691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128896, rend_intergenic: 123156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135946, rend_intergenic: 132597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157602, rend_intergenic: 154094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185930, rend_intergenic: 182316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199997
-exon list size: 530


building trellis

0.2    
0.4    
0.6    
0.8    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.6    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
7.0    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.3    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.8    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.8    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.4    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 79738, rend_intergenic: 75874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82507, rend_intergenic: 81334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95121, rend_intergenic: 91501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101762, rend_intergenic: 95691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128896, rend_intergenic: 123156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135946, rend_intergenic: 132597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157602, rend_intergenic: 154094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185930, rend_intergenic: 182316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support