-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_174

-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 GlimmerHMM_glimmerT_61450-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61450-T1 107-267-terminal-1 is invalid.
Valid prediction for GlimmerHMM_glimmerT_61451-T1
Couldn't classify 107, 186
Sorry, prediction Augustus_model.g40868.t1 fails validation.
(ACT)	 AG	107-186	GT	AGG
(TTT)	 AG	1266-1323	GT	CTG
(CGG)	 AG	1466-1611	GT	GGG
(TAC)	 AG	1772-1809	GT	TGG
(GGG)	 AG	1909-2076	GT	GGG
(GCT)	 AG	2320-2433	GT	AGG
(AAG)	 AG	2701-2831	GT	AGG
(ATC)	 AG	3337-3459	GT	AGG
(GGT)	 AG	3645-3650	AT	AGA
-recovered Augustus_model.g40868.t1, terminal, 3645, 3650
-recovered Augustus_model.g40868.t1, internal, 107, 186
-recovered Augustus_model.g40868.t1, internal, 1266, 1323
-recovered Augustus_model.g40868.t1, internal, 1466, 1611
-recovered Augustus_model.g40868.t1, internal, 1772, 1809
-recovered Augustus_model.g40868.t1, internal, 1909, 2076
-recovered Augustus_model.g40868.t1, internal, 2320, 2433
-recovered Augustus_model.g40868.t1, internal, 2701, 2831
-recovered Augustus_model.g40868.t1, internal, 3337, 3459
Couldn't classify 107, 186
Sorry, prediction snap_scaffold_174-snap.1-T1 fails validation.
(ACT)	 AG	107-186	GT	AGG
(TTT)	 AG	1266-1371	GT	TTG
(CGG)	 AG	1466-1611	GT	GGG
(TAC)	 AG	1772-1809	GT	TGG
(GGG)	 AG	1909-2076	GT	GGG
(GCT)	 AG	2320-2433	GT	AGG
(AAG)	 AG	2701-2831	GT	AGG
(GTA)	 AG	3054-3152	GT	TCG
(ATC)	 AG	3337-3459	GT	AGG
(ATG)	 AG	4289-4346	GT	TGG
(TAG)	 AG	4478-4602	CC	GAC
-recovered snap_scaffold_174-snap.1-T1, initial, 4289, 4346
-recovered snap_scaffold_174-snap.1-T1, terminal, 4478, 4602
-recovered snap_scaffold_174-snap.1-T1, internal, 107, 186
-recovered snap_scaffold_174-snap.1-T1, internal, 1266, 1371
-recovered snap_scaffold_174-snap.1-T1, internal, 1466, 1611
-recovered snap_scaffold_174-snap.1-T1, internal, 1772, 1809
-recovered snap_scaffold_174-snap.1-T1, internal, 1909, 2076
-recovered snap_scaffold_174-snap.1-T1, internal, 2320, 2433
-recovered snap_scaffold_174-snap.1-T1, internal, 2701, 2831
-recovered snap_scaffold_174-snap.1-T1, internal, 3054, 3152
-recovered snap_scaffold_174-snap.1-T1, internal, 3337, 3459
-recovered snap_scaffold_174-snap.1-T1, internal, 4289, 4346
Couldn't classify 107, 186
Sorry, prediction GeneMark_model.106825_t fails validation.
(ACT)	 AG	107-186	GT	AGG
(TTT)	 AG	1266-1448	GT	AAG
(GAG)	 AG	1607-1620	GT	CAG
(GGG)	 AG	1909-2076	GT	GGG
(GCT)	 AG	2320-2433	GT	AGG
(AAG)	 AG	2701-2822	GT	AAG
(GTA)	 AG	3054-3152	GT	TCG
(ATC)	 AG	3337-3459	GT	AGG
(ATG)	 AG	4289-4299	GT	GGG
(ACC)	 AG	4470-4602	CC	GAC
-recovered GeneMark_model.106825_t, initial, 4289, 4299
-recovered GeneMark_model.106825_t, terminal, 1266, 1448
-recovered GeneMark_model.106825_t, terminal, 4470, 4602
-recovered GeneMark_model.106825_t, internal, 107, 186
-recovered GeneMark_model.106825_t, internal, 1266, 1448
-recovered GeneMark_model.106825_t, internal, 1607, 1620
-recovered GeneMark_model.106825_t, internal, 1909, 2076
-recovered GeneMark_model.106825_t, internal, 2320, 2433
-recovered GeneMark_model.106825_t, internal, 2701, 2822
-recovered GeneMark_model.106825_t, internal, 3054, 3152
-recovered GeneMark_model.106825_t, internal, 3337, 3459
-recovered GeneMark_model.106825_t, internal, 4289, 4299

-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.106826_t
Valid prediction for GlimmerHMM_glimmerT_61452-T1
Valid prediction for snap_scaffold_174-snap.2-T1
Valid prediction for Augustus_model.g40869.t1

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

-building trellis in range 1 - 10806
-exon list size: 46


building trellis

2.1    
4.2    
6.2    
8.3    
10.4    
12.5    
14.6    
16.7    
18.8    
20.8    
22.9    
25.0    
27.1    
29.2    
31.2    
33.3    
35.4    
37.5    
39.6    
41.7    
43.8    
45.8    
47.9    
50.0    
52.1    
54.2    
56.2    
58.3    
60.4    
62.5    
64.6    
66.7    
68.8    
70.8    
72.9    
75.0    
77.1    
79.2    
81.2    
83.3    
85.4    
87.5    
89.6    
91.7    
93.8    
95.8    
97.9    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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