-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_616

-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 482, 617
Sorry, prediction snap_scaffold_616-snap.1-T1 fails validation.
(CCG)	 AG	482-617	GT	TAG
(GTA)	 AG	1631-1765	CT	GAC
-recovered snap_scaffold_616-snap.1-T1, terminal, 1631, 1765
-recovered snap_scaffold_616-snap.1-T1, internal, 482, 617
Valid prediction for GeneMark_model.108047_t
Couldn't classify 5252, 5358
Sorry, prediction GeneMark_model.108049_t fails validation.
(ATG)	 TG	3870-3976	GT	AGG
(AGA)	 AG	4462-4579	GT	GGG
(AAG)	 AG	4741-4862	GT	GGG
(GGA)	 AG	4889-4897	GT	GCG
(GAA)	 AG	4955-5113	GT	GGG
(GAT)	 AG	5252-5358	GC	CTG
-recovered GeneMark_model.108049_t, initial, 3870, 3976
-recovered GeneMark_model.108049_t, internal, 4462, 4579
-recovered GeneMark_model.108049_t, internal, 4741, 4862
-recovered GeneMark_model.108049_t, internal, 4889, 4897
-recovered GeneMark_model.108049_t, internal, 4955, 5113
-recovered GeneMark_model.108049_t, internal, 5252, 5358
Valid prediction for Augustus_model.g41244.t1
Couldn't classify 17, 40
Sorry, prediction GeneMark_model.108046_t fails validation.
(TGA)	 AG	17-40	GT	GAG
(AAA)	 AG	75-140	GT	GAG
(GGG)	 AG	181-216	GT	GAG
(AAA)	 AG	251-316	GT	GAG
(GGG)	 AG	351-413	GT	CCG
(GAC)	 AG	501-618	TG	AGT
-recovered GeneMark_model.108046_t, terminal, 501, 618
-recovered GeneMark_model.108046_t, internal, 17, 40
-recovered GeneMark_model.108046_t, internal, 75, 140
-recovered GeneMark_model.108046_t, internal, 181, 216
-recovered GeneMark_model.108046_t, internal, 251, 316
-recovered GeneMark_model.108046_t, internal, 351, 413
Couldn't classify 4955, 5113
Sorry, prediction snap_scaffold_616-snap.2-T1 fails validation.
(ATG)	 GG	2531-2616	GT	AGG
(TTG)	 AG	2785-2912	GT	AGG
(TGT)	 AG	3823-3976	GT	AGG
(AGA)	 AG	4462-4579	GT	GGG
(AAG)	 AG	4741-4862	GT	GGG
(GAA)	 AG	4955-5113	GT	GGG
-recovered snap_scaffold_616-snap.2-T1, initial, 2531, 2616
-recovered snap_scaffold_616-snap.2-T1, terminal, 2785, 2912
-recovered snap_scaffold_616-snap.2-T1, internal, 2785, 2912
-recovered snap_scaffold_616-snap.2-T1, internal, 3823, 3976
-recovered snap_scaffold_616-snap.2-T1, internal, 4462, 4579
-recovered snap_scaffold_616-snap.2-T1, internal, 4741, 4862
-recovered snap_scaffold_616-snap.2-T1, internal, 4955, 5113
Couldn't classify 3963, 3976
Couldn't classify 4955, 5093
Sorry, prediction pasa_asmbl_49409.p1 fails validation.
(CTC)	 AC	3963-3976	GT	AGG
(AGA)	 AG	4462-4579	GT	GGG
(AAG)	 AG	4741-4862	GT	GGG
(GAA)	 AG	4955-5093	CC	CCC
-recovered pasa_asmbl_49409.p1, internal, 4462, 4579
-recovered pasa_asmbl_49409.p1, internal, 4741, 4862
Couldn't classify 4955, 5113
Sorry, prediction GlimmerHMM_glimmerT_62052-T1 fails validation.
(ATG)	 CG	704-851	GT	CGG
(TGT)	 AG	3823-3976	GT	AGG
(AGA)	 AG	4462-4579	GT	GGG
(AAG)	 AG	4741-4862	GT	GGG
(GAA)	 AG	4955-5113	GT	GGG
-recovered GlimmerHMM_glimmerT_62052-T1, initial, 704, 851
-recovered GlimmerHMM_glimmerT_62052-T1, internal, 3823, 3976
-recovered GlimmerHMM_glimmerT_62052-T1, internal, 4462, 4579
-recovered GlimmerHMM_glimmerT_62052-T1, internal, 4741, 4862
-recovered GlimmerHMM_glimmerT_62052-T1, internal, 4955, 5113

-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.108048_t

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

-building trellis in range 1 - 5367
-exon list size: 36


building trellis

2.6    
5.3    
7.9    
10.5    
13.2    
15.8    
18.4    
21.1    
23.7    
26.3    
28.9    
31.6    
34.2    
36.8    
39.5    
42.1    
44.7    
47.4    
50.0    
52.6    
55.3    
57.9    
60.5    
63.2    
65.8    
68.4    
71.1    
73.7    
76.3    
78.9    
81.6    
84.2    
86.8    
89.5    
92.1    
94.7    
97.4    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support