-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_963

-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_62368-T1
Couldn't classify 1467, 1502
Sorry, prediction snap_scaffold_963-snap.2-T1 fails validation.
(GAC)	 AG	1467-1502	GT	GGG
(TTG)	 AG	1822-1860	GT	CGG
(TTT)	 AG	1980-2039	GT	ATG
(GAG)	 AG	2162-2231	GT	CAG
(ATA)	 AG	2928-3088	GC	AAG
-recovered snap_scaffold_963-snap.2-T1, terminal, 2928, 3088
-recovered snap_scaffold_963-snap.2-T1, internal, 1467, 1502
-recovered snap_scaffold_963-snap.2-T1, internal, 1822, 1860
-recovered snap_scaffold_963-snap.2-T1, internal, 1980, 2039
-recovered snap_scaffold_963-snap.2-T1, internal, 2162, 2231
-recovered snap_scaffold_963-snap.2-T1, internal, 2928, 3088
Couldn't classify 1822, 1860
Sorry, prediction Augustus_model.g41461.t1 fails validation.
(TTG)	 AG	1822-1860	GT	CGG
(CCA)	 AG	1972-2039	GT	ATG
(GAG)	 AG	2162-2248	AT	GAA
-recovered Augustus_model.g41461.t1, terminal, 2162, 2248
-recovered Augustus_model.g41461.t1, internal, 1822, 1860
-recovered Augustus_model.g41461.t1, internal, 1972, 2039
Valid prediction for GeneMark_model.108675_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 GeneMark_model.108674_t
Couldn't classify 32, 114
Sorry, prediction snap_scaffold_963-snap.3-T1 fails validation.
(ATC)	 AG	32-114	GT	AGG
(ACT)	 AG	228-402	GA	GAG
-recovered snap_scaffold_963-snap.3-T1, terminal, 228, 402
-recovered snap_scaffold_963-snap.3-T1, internal, 32, 114
Couldn't classify 11, 114
Sorry, prediction GeneMark_model.108676_t fails validation.
(CGT)	 AG	11-114	GT	AGG
(ACT)	 AG	228-402	GA	GAG
-recovered GeneMark_model.108676_t, terminal, 228, 402
-recovered GeneMark_model.108676_t, internal, 11, 114
Couldn't classify 8, 114
Sorry, prediction GlimmerHMM_glimmerT_62369-T1 fails validation.
(GAG)	 AG	8-114	GT	AGG
(ACT)	 AG	228-402	GA	GAG
-recovered GlimmerHMM_glimmerT_62369-T1, terminal, 228, 402
-recovered GlimmerHMM_glimmerT_62369-T1, internal, 8, 114
Couldn't classify 1, 114
Sorry, prediction Augustus_model.g41462.t1 fails validation.
(GTT)	 AG	1-114	GT	AGG
(ACT)	 AG	228-402	GA	GAG
-recovered Augustus_model.g41462.t1, terminal, 228, 402
Couldn't classify 2933, 3070
Sorry, prediction snap_scaffold_963-snap.1-T1 fails validation.
(ATG)	 TG	2597-2729	GT	AGG
(CAA)	 AG	2933-3070	GT	GAG
-recovered snap_scaffold_963-snap.1-T1, initial, 2597, 2729
-recovered snap_scaffold_963-snap.1-T1, internal, 2933, 3070

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

-building trellis in range 1 - 3783
-exon list size: 41


building trellis

2.3    
4.7    
7.0    
9.3    
11.6    
14.0    
16.3    
18.6    
20.9    
23.3    
25.6    
27.9    
30.2    
32.6    
34.9    
37.2    
39.5    
41.9    
44.2    
46.5    
48.8    
51.2    
53.5    
55.8    
58.1    
60.5    
62.8    
65.1    
67.4    
69.8    
72.1    
74.4    
76.7    
79.1    
81.4    
83.7    
86.0    
88.4    
90.7    
93.0    
95.3    
97.7    
-found 3 predictions from path traversal
GOT 5prime partial gene.

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