-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_590

-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: +)Couldn't classify 5374, 5505
Sorry, prediction snap_scaffold_590-snap.2-T1 fails validation.
(ATG)	 AC	1367-1371	GT	CAG
(AGA)	 AG	1975-2074	GT	CGG
(CGC)	 AG	2710-2880	GT	AGG
(GTG)	 AG	3222-3407	GT	AGG
(ATC)	 AG	3676-3812	GT	GAG
(TGA)	 AG	4011-4191	GT	CAG
(GTC)	 AG	4500-4659	GT	TGG
(ACC)	 AG	4936-5058	GT	AGG
(GCT)	 AG	5374-5505	GT	AAG
-recovered snap_scaffold_590-snap.2-T1, initial, 1367, 1371
add_exon() Sorry, snap_scaffold_590-snap.2-T1 3676-3812-terminal-2 is invalid.
-recovered snap_scaffold_590-snap.2-T1, terminal, 3676, 3812
-recovered snap_scaffold_590-snap.2-T1, internal, 1975, 2074
-recovered snap_scaffold_590-snap.2-T1, internal, 2710, 2880
-recovered snap_scaffold_590-snap.2-T1, internal, 3222, 3407
-recovered snap_scaffold_590-snap.2-T1, internal, 3676, 3812
-recovered snap_scaffold_590-snap.2-T1, internal, 4011, 4191
-recovered snap_scaffold_590-snap.2-T1, internal, 4500, 4659
-recovered snap_scaffold_590-snap.2-T1, internal, 4936, 5058
-recovered snap_scaffold_590-snap.2-T1, internal, 5374, 5505
Couldn't classify 59, 191
Sorry, prediction snap_scaffold_590-snap.1-T1 fails validation.
(CGG)	 AG	59-191	GT	AGG
(GTA)	 AG	376-606	AG	GAA
-recovered snap_scaffold_590-snap.1-T1, terminal, 376, 606
-recovered snap_scaffold_590-snap.1-T1, internal, 59, 191
Couldn't classify 5529, 5539
Sorry, prediction GeneMark_model.107994_t fails validation.
(ATG)	 GG	3082-3084	GT	TGG
(GTG)	 AG	3222-3407	GT	AGG
(ATC)	 AG	3676-3812	GT	GAG
(TGA)	 AG	4011-4191	GT	CAG
(GTC)	 AG	4500-4659	GT	TGG
(ACC)	 AG	4936-5058	GT	AGG
(GCT)	 AG	5374-5505	GT	AAG
(CGT)	 AG	5529-5539	GT	CTG
-recovered GeneMark_model.107994_t, initial, 3082, 3084
add_exon() Sorry, GeneMark_model.107994_t 3676-3812-terminal-2 is invalid.
-recovered GeneMark_model.107994_t, terminal, 3676, 3812
-recovered GeneMark_model.107994_t, internal, 3222, 3407
-recovered GeneMark_model.107994_t, internal, 3676, 3812
-recovered GeneMark_model.107994_t, internal, 4011, 4191
-recovered GeneMark_model.107994_t, internal, 4500, 4659
-recovered GeneMark_model.107994_t, internal, 4936, 5058
-recovered GeneMark_model.107994_t, internal, 5374, 5505
-recovered GeneMark_model.107994_t, internal, 5529, 5539
Valid prediction for GlimmerHMM_glimmerT_62026-T1
Couldn't classify 5374, 5505
Sorry, prediction Augustus_model.g41228.t1 fails validation.
(ATG)	 TG	2731-2880	GT	AGG
(GTG)	 AG	3222-3407	GT	AGG
(ATC)	 AG	3676-3812	GT	GAG
(TGA)	 AG	4011-4212	GT	TGG
(GTC)	 AG	4500-4659	GT	TGG
(ACC)	 AG	4936-5058	GT	AGG
(GCT)	 AG	5374-5505	GT	AAG
-recovered Augustus_model.g41228.t1, initial, 2731, 2880
add_exon() Sorry, Augustus_model.g41228.t1 3676-3812-terminal-2 is invalid.
-recovered Augustus_model.g41228.t1, terminal, 3676, 3812
-recovered Augustus_model.g41228.t1, internal, 3222, 3407
-recovered Augustus_model.g41228.t1, internal, 3676, 3812
-recovered Augustus_model.g41228.t1, internal, 4011, 4212
-recovered Augustus_model.g41228.t1, internal, 4500, 4659
-recovered Augustus_model.g41228.t1, internal, 4936, 5058
-recovered Augustus_model.g41228.t1, internal, 5374, 5505
Couldn't classify 5374, 5449
Sorry, prediction GlimmerHMM_glimmerT_62027-T1 fails validation.
(ATG)	 CC	4021-4191	GT	CAG
(GTC)	 AG	4500-4659	GT	TGG
(ACC)	 AG	4936-5058	GT	AGG
(GCT)	 AG	5374-5449	GT	AGG
-recovered GlimmerHMM_glimmerT_62027-T1, initial, 4021, 4191
-recovered GlimmerHMM_glimmerT_62027-T1, internal, 4500, 4659
-recovered GlimmerHMM_glimmerT_62027-T1, internal, 4936, 5058
-recovered GlimmerHMM_glimmerT_62027-T1, internal, 5374, 5449

-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.g41227.t1
Valid prediction for GeneMark_model.107993_t
Valid prediction for GlimmerHMM_glimmerT_62025-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 5577
-exon list size: 38


building trellis

2.5    
5.0    
7.5    
10.0    
12.5    
15.0    
17.5    
20.0    
22.5    
25.0    
27.5    
30.0    
32.5    
35.0    
37.5    
40.0    
42.5    
45.0    
47.5    
50.0    
52.5    
55.0    
57.5    
60.0    
62.5    
65.0    
67.5    
70.0    
72.5    
75.0    
77.5    
80.0    
82.5    
85.0    
87.5    
90.0    
92.5    
95.0    
97.5    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support