-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_70

-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 Augustus_model.g40695.t1
Valid prediction for GeneMark_model.106380_t
Valid prediction for GlimmerHMM_glimmerT_61174-T1
Valid prediction for HiQ_model.g40696.t1
Valid prediction for snap_scaffold_70-snap.3-T1
Valid prediction for GeneMark_model.106378_t
Couldn't classify 3639, 3770
Sorry, prediction pasa_asmbl_51546.p1 fails validation.
(CAG)	 CC	3639-3770	GT	AGG
(ACG)	 AG	3876-3967	GT	CGG
(AAA)	 AG	4397-4542	GT	CAG
(TTG)	 AG	5227-5415	GT	AGG
(AGA)	 AG	6760-6767	AG	AGA
-recovered pasa_asmbl_51546.p1, terminal, 6760, 6767
-recovered pasa_asmbl_51546.p1, internal, 3876, 3967
-recovered pasa_asmbl_51546.p1, internal, 4397, 4542
-recovered pasa_asmbl_51546.p1, internal, 5227, 5415
Valid prediction for snap_scaffold_70-snap.5-T1
Valid prediction for snap_scaffold_70-snap.1-T1
Valid prediction for CodingQuarry_transcript_57635-T1
Couldn't classify 1585, 1613
Sorry, prediction GeneMark_model.106376_t fails validation.
(AGG)	 AG	1585-1613	GT	CAG
(AGA)	 AG	1635-1643	GT	GAG
(CTG)	 AG	2981-3098	GT	AGG
(GTG)	 AG	3642-3770	GT	AGG
(ACG)	 AG	3876-4013	CC	AAC
-recovered GeneMark_model.106376_t, terminal, 3876, 4013
-recovered GeneMark_model.106376_t, internal, 1585, 1613
-recovered GeneMark_model.106376_t, internal, 1635, 1643
-recovered GeneMark_model.106376_t, internal, 2981, 3098
-recovered GeneMark_model.106376_t, internal, 3642, 3770
Valid prediction for GlimmerHMM_glimmerT_61175-T1
Valid prediction for CodingQuarry_transcript_57637-T1
Valid prediction for Augustus_model.g40698.t1
Valid prediction for snap_scaffold_70-snap.2-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 GeneMark_model.106377_t
Couldn't classify 747, 779
Sorry, prediction GeneMark_model.106383_t fails validation.
(AGG)	 AG	747-779	GT	GGG
(AGA)	 AG	809-874	GT	GAG
(ATG)	 AG	907-969	GT	CGG
(GAG)	 AG	992-1012	GT	GTG
(AGG)	 AG	1049-1093	GT	AGG
(AAC)	 AG	1140-1145	GT	GAG
(GAC)	 AG	1372-1386	GT	GGG
(GAT)	 AG	1500-1541	GT	GAG
(AAA)	 AG	1563-1578	GT	GAG
(GGA)	 AG	2011-2087	GT	GGG
(AAA)	 AG	2115-2123	GT	GAG
(AGT)	 AG	2163-2183	GT	AGG
(CAG)	 AG	2205-2234	GT	GAG
(GGA)	 AG	2278-2332	AT	AAA
-recovered GeneMark_model.106383_t, initial, 907, 969
-recovered GeneMark_model.106383_t, terminal, 809, 874
-recovered GeneMark_model.106383_t, terminal, 2278, 2332
-recovered GeneMark_model.106383_t, internal, 747, 779
-recovered GeneMark_model.106383_t, internal, 809, 874
-recovered GeneMark_model.106383_t, internal, 907, 969
-recovered GeneMark_model.106383_t, internal, 992, 1012
-recovered GeneMark_model.106383_t, internal, 1049, 1093
-recovered GeneMark_model.106383_t, internal, 1140, 1145
-recovered GeneMark_model.106383_t, internal, 1372, 1386
-recovered GeneMark_model.106383_t, internal, 1500, 1541
-recovered GeneMark_model.106383_t, internal, 1563, 1578
-recovered GeneMark_model.106383_t, internal, 2011, 2087
-recovered GeneMark_model.106383_t, internal, 2115, 2123
-recovered GeneMark_model.106383_t, internal, 2163, 2183
-recovered GeneMark_model.106383_t, internal, 2205, 2234
Valid prediction for GeneMark_model.106381_t
Valid prediction for snap_scaffold_70-snap.6-T1
Valid prediction for Augustus_model.g40697.t1
Valid prediction for GeneMark_model.106382_t
Couldn't classify 451, 590
Sorry, prediction snap_scaffold_70-snap.7-T1 fails validation.
(GTC)	 AG	451-590	GT	GTG
(GGG)	 AG	1473-1587	GT	TTG
(TGA)	 AG	1705-1721	GG	AAG
-recovered snap_scaffold_70-snap.7-T1, terminal, 1705, 1721
-recovered snap_scaffold_70-snap.7-T1, internal, 451, 590
-recovered snap_scaffold_70-snap.7-T1, internal, 1473, 1587
Valid prediction for snap_scaffold_70-snap.4-T1
Valid prediction for GeneMark_model.106379_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24707, rend_intergenic: 22133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 25000
-exon list size: 120


building trellis

0.8    
1.6    
2.5    
3.3    
4.1    
4.9    
5.7    
6.6    
7.4    
8.2    
9.0    
9.8    
10.7    
11.5    
12.3    
13.1    
13.9    
14.8    
15.6    
16.4    
17.2    
18.0    
18.9    
19.7    
20.5    
21.3    
22.1    
23.0    
23.8    
24.6    
25.4    
26.2    
27.0    
27.9    
28.7    
29.5    
30.3    
31.1    
32.0    
32.8    
33.6    
34.4    
35.2    
36.1    
36.9    
37.7    
38.5    
39.3    
40.2    
41.0    
41.8    
42.6    
43.4    
44.3    
45.1    
45.9    
46.7    
47.5    
48.4    
49.2    
50.0    
50.8    
51.6    
52.5    
53.3    
54.1    
54.9    
55.7    
56.6    
57.4    
58.2    
59.0    
59.8    
60.7    
61.5    
62.3    
63.1    
63.9    
64.8    
65.6    
66.4    
67.2    
68.0    
68.9    
69.7    
70.5    
71.3    
72.1    
73.0    
73.8    
74.6    
75.4    
76.2    
77.0    
77.9    
78.7    
79.5    
80.3    
81.1    
82.0    
82.8    
83.6    
84.4    
85.2    
86.1    
86.9    
87.7    
88.5    
89.3    
90.2    
91.0    
91.8    
92.6    
93.4    
94.3    
95.1    
95.9    
96.7    
97.5    
98.4    
99.2    
-found 4 predictions from path traversal
Error with prediction: snap lend_intergenic: 24707, rend_intergenic: 22133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support