-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_2933088-3047379

-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.90205_t
Valid prediction for snap_scaffold_23-snap.561-T1
Valid prediction for GeneMark_model.90210_t
Valid prediction for snap_scaffold_23-snap.569-T1
Valid prediction for snap_scaffold_23-snap.556-T1
Valid prediction for GlimmerHMM_glimmerT_51930-T1
Valid prediction for GeneMark_model.90212_t
Valid prediction for GlimmerHMM_glimmerT_51934-T1
Valid prediction for GlimmerHMM_glimmerT_51935-T1
Valid prediction for Augustus_model.g34909.t1
Valid prediction for GlimmerHMM_glimmerT_51943-T1
Valid prediction for GeneMark_model.90200_t
Valid prediction for GeneMark_model.90204_t
Valid prediction for snap_scaffold_23-snap.577-T1
Valid prediction for GeneMark_model.90208_t
Valid prediction for snap_scaffold_23-snap.578-T1
Valid prediction for GlimmerHMM_glimmerT_51939-T1
Valid prediction for GeneMark_model.90202_t
Valid prediction for GeneMark_model.90198_t
Valid prediction for GeneMark_model.90213_t
Valid prediction for GeneMark_model.90199_t
Valid prediction for GeneMark_model.90217_t
Valid prediction for snap_scaffold_23-snap.570-T1
Valid prediction for snap_scaffold_23-snap.558-T1
Valid prediction for GeneMark_model.90197_t
Valid prediction for GlimmerHMM_glimmerT_51941-T1
Valid prediction for snap_scaffold_23-snap.566-T1
Valid prediction for Augustus_model.g34905.t1
Valid prediction for GlimmerHMM_glimmerT_51946-T1
Valid prediction for Augustus_model.g34904.t1
Valid prediction for GeneMark_model.90195_t

-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 Augustus_model.g34912.t1
Valid prediction for GlimmerHMM_glimmerT_51933-T1
Valid prediction for GlimmerHMM_glimmerT_51931-T1
Valid prediction for snap_scaffold_23-snap.557-T1
Couldn't classify 49674, 49723
Couldn't classify 51298, 51299
Sorry, prediction pasa_asmbl_31494.p1 fails validation.
(TCT)	 CG	49674-49723	GT	TGG
(TGG)	 AG	50063-50204	GT	GGG
(GTG)	 AG	50396-50575	GT	AGG
(TCA)	 AG	50748-50949	GC	GTG
(AAA)	 AG	51298-51299	AC	AAA
-recovered pasa_asmbl_31494.p1, internal, 50063, 50204
-recovered pasa_asmbl_31494.p1, internal, 50396, 50575
-recovered pasa_asmbl_31494.p1, internal, 50748, 50949
Valid prediction for CodingQuarry_transcript_35535-T1
Valid prediction for Augustus_model.g34907.t1
Valid prediction for GeneMark_model.90196_t
Valid prediction for snap_scaffold_23-snap.576-T1
Valid prediction for pasa_asmbl_31490.p1
Couldn't classify 44711, 44976
Sorry, prediction pasa_asmbl_31499.p1 fails validation.
(CCC)	 CC	44711-44976	GT	GGG
(GAT)	 AG	45564-45750	AT	AGA
-recovered pasa_asmbl_31499.p1, terminal, 45564, 45750
Valid prediction for GlimmerHMM_glimmerT_51949-T1
Couldn't classify 51298, 51299
Sorry, prediction CodingQuarry_transcript_35534-T1 fails validation.
(ATG)	 AG	50082-50204	GT	GGG
(GTG)	 AG	50396-50575	GT	AGG
(TCA)	 AG	50748-50949	GC	GTG
(AAA)	 AG	51298-51299	AC	AAA
-recovered CodingQuarry_transcript_35534-T1, initial, 50082, 50204
-recovered CodingQuarry_transcript_35534-T1, internal, 50082, 50204
-recovered CodingQuarry_transcript_35534-T1, internal, 50396, 50575
-recovered CodingQuarry_transcript_35534-T1, internal, 50748, 50949
Valid prediction for GeneMark_model.90207_t
Valid prediction for snap_scaffold_23-snap.560-T1
Valid prediction for GlimmerHMM_glimmerT_51948-T1
Valid prediction for GlimmerHMM_glimmerT_51945-T1
Valid prediction for Augustus_model.g34908.t1
Valid prediction for GlimmerHMM_glimmerT_51944-T1
Valid prediction for GlimmerHMM_glimmerT_51937-T1
Valid prediction for GeneMark_model.90215_t
Couldn't classify 72189, 72326
Sorry, prediction pasa_asmbl_31485.p1 fails validation.
(GGC)	 AG	72189-72326	GT	AGG
(CTC)	 AG	75013-75103	GT	AAG
(GTT)	 AG	75414-75591	GT	CGG
(GGA)	 AG	78519-78618	GA	AGG
-recovered pasa_asmbl_31485.p1, terminal, 78519, 78618
-recovered pasa_asmbl_31485.p1, internal, 72189, 72326
-recovered pasa_asmbl_31485.p1, internal, 75013, 75103
-recovered pasa_asmbl_31485.p1, internal, 75414, 75591
Valid prediction for snap_scaffold_23-snap.582-T1
Valid prediction for snap_scaffold_23-snap.567-T1
Valid prediction for snap_scaffold_23-snap.581-T1
Valid prediction for CodingQuarry_transcript_35533-T1
Couldn't classify 21899, 22042
Couldn't classify 25807, 25834
Sorry, prediction pasa_asmbl_31501.p1 fails validation.
(GCA)	 AG	21899-22042	GT	AGG
(GTG)	 AG	22279-22377	GT	AGG
(AGA)	 AG	22511-22717	GT	AGG
(GTG)	 AG	22851-22955	GT	AGG
(GAG)	 AG	23082-23234	GT	AGG
(CTC)	 AG	23356-23523	GT	AGG
(GTG)	 AG	23795-23968	GT	AGG
(GAG)	 AG	24393-24482	GT	AGG
(GTT)	 AG	24631-24714	GT	AGG
(ATC)	 AG	24834-24952	GT	AGG
(GAA)	 AG	25072-25180	GT	TGG
(ATG)	 AG	25383-25546	GT	AAG
(ACG)	 AG	25807-25834	AC	AGA
-recovered pasa_asmbl_31501.p1, initial, 25383, 25546
-recovered pasa_asmbl_31501.p1, internal, 21899, 22042
-recovered pasa_asmbl_31501.p1, internal, 22279, 22377
-recovered pasa_asmbl_31501.p1, internal, 22511, 22717
-recovered pasa_asmbl_31501.p1, internal, 22851, 22955
-recovered pasa_asmbl_31501.p1, internal, 23082, 23234
-recovered pasa_asmbl_31501.p1, internal, 23356, 23523
-recovered pasa_asmbl_31501.p1, internal, 23795, 23968
-recovered pasa_asmbl_31501.p1, internal, 24393, 24482
-recovered pasa_asmbl_31501.p1, internal, 24631, 24714
-recovered pasa_asmbl_31501.p1, internal, 24834, 24952
-recovered pasa_asmbl_31501.p1, internal, 25072, 25180
-recovered pasa_asmbl_31501.p1, internal, 25383, 25546
Valid prediction for GeneMark_model.90201_t
Valid prediction for GlimmerHMM_glimmerT_51950-T1
Valid prediction for snap_scaffold_23-snap.562-T1
Valid prediction for GlimmerHMM_glimmerT_51940-T1
Valid prediction for GeneMark_model.90216_t
Valid prediction for GeneMark_model.90209_t
Valid prediction for Augustus_model.g34911.t1
Valid prediction for snap_scaffold_23-snap.575-T1
Valid prediction for snap_scaffold_23-snap.563-T1
Valid prediction for GlimmerHMM_glimmerT_51951-T1
Valid prediction for GeneMark_model.90218_t
Valid prediction for GlimmerHMM_glimmerT_51947-T1
Valid prediction for CodingQuarry_transcript_35531-T1
Valid prediction for snap_scaffold_23-snap.580-T1
Valid prediction for snap_scaffold_23-snap.564-T1
Valid prediction for snap_scaffold_23-snap.579-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_51936-T1
Valid prediction for HiQ_model.g34910.t1
Valid prediction for Augustus_model.g34914.t1
Valid prediction for Augustus_model.g34913.t1
Valid prediction for snap_scaffold_23-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_51932-T1
Valid prediction for snap_scaffold_23-snap.559-T1
Valid prediction for GlimmerHMM_glimmerT_51942-T1
Valid prediction for GlimmerHMM_glimmerT_51938-T1
Valid prediction for Augustus_model.g34906.t1
Valid prediction for GeneMark_model.90206_t
Valid prediction for snap_scaffold_23-snap.568-T1
Valid prediction for snap_scaffold_23-snap.572-T1
Valid prediction for snap_scaffold_23-snap.574-T1
Valid prediction for GeneMark_model.90214_t
Valid prediction for snap_scaffold_23-snap.573-T1
Valid prediction for GeneMark_model.90203_t
Valid prediction for snap_scaffold_23-snap.565-T1
Valid prediction for snap_scaffold_23-snap.583-T1
Valid prediction for GeneMark_model.90211_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 49871, rend_intergenic: 48830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 114292
-exon list size: 381


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
4.2    
4.4    
4.7    
5.0    
5.2    
5.5    
5.7    
6.0    
6.3    
6.5    
6.8    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
17.0    
17.2    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.7    
23.0    
23.2    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.1    
31.3    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.7    
68.9    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.8    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.8    
83.0    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.7    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 49871, rend_intergenic: 48830  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