-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_489

-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_61910-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61910-T1 376-920-terminal-1 is invalid.
Couldn't classify 376, 577
Sorry, prediction GeneMark_model.107771_t fails validation.
(AAA)	 AG	376-577	GT	GGG
(ACT)	 AG	624-630	AG	AGA
-recovered GeneMark_model.107771_t, terminal, 624, 630
-recovered GeneMark_model.107771_t, internal, 376, 577
Valid prediction for GeneMark_model.107773_t
Couldn't classify 376, 542
Sorry, prediction Augustus_model.g41154.t1 fails validation.
(AAA)	 AG	376-542	GT	AGG
(AGG)	 AG	1349-1445	GT	AGG
(GCC)	 AG	1842-1939	GT	TGG
(AGC)	 AG	2088-2180	GT	GGG
(GGC)	 AG	3482-3552	GT	AGG
(GTA)	 AG	3937-4044	GT	AGG
(CGG)	 AG	4222-4386	GT	ACG
(CTG)	 AG	4464-4477	GT	TGG
(TAT)	 AG	4898-5012	GT	AGG
(ACT)	 AG	5194-5353	CG	AGC
-recovered Augustus_model.g41154.t1, terminal, 5194, 5353
-recovered Augustus_model.g41154.t1, internal, 376, 542
-recovered Augustus_model.g41154.t1, internal, 1349, 1445
-recovered Augustus_model.g41154.t1, internal, 1842, 1939
-recovered Augustus_model.g41154.t1, internal, 2088, 2180
-recovered Augustus_model.g41154.t1, internal, 3482, 3552
-recovered Augustus_model.g41154.t1, internal, 3937, 4044
-recovered Augustus_model.g41154.t1, internal, 4222, 4386
-recovered Augustus_model.g41154.t1, internal, 4464, 4477
-recovered Augustus_model.g41154.t1, internal, 4898, 5012
Couldn't classify 5194, 5324
Sorry, prediction GlimmerHMM_glimmerT_61911-T1 fails validation.
(ATG)	 AC	1400-1445	GT	AGG
(GCC)	 AG	1842-1939	GT	TGG
(AGC)	 AG	2088-2180	GT	GGG
(GGC)	 AG	3482-3552	GT	AGG
(GTA)	 AG	3937-4044	GT	AGG
(CGG)	 AG	4222-4386	GT	ACG
(ACT)	 AG	5194-5324	GT	AGG
-recovered GlimmerHMM_glimmerT_61911-T1, initial, 1400, 1445
-recovered GlimmerHMM_glimmerT_61911-T1, internal, 1842, 1939
-recovered GlimmerHMM_glimmerT_61911-T1, internal, 2088, 2180
-recovered GlimmerHMM_glimmerT_61911-T1, internal, 3482, 3552
-recovered GlimmerHMM_glimmerT_61911-T1, internal, 3937, 4044
-recovered GlimmerHMM_glimmerT_61911-T1, internal, 4222, 4386
-recovered GlimmerHMM_glimmerT_61911-T1, internal, 5194, 5324
Couldn't classify 375, 542
Sorry, prediction pasa_asmbl_43719.p1 fails validation.
(GAA)	 CA	375-542	GT	AGG
(AGG)	 AG	1349-1445	GT	AGG
(GCC)	 AG	1842-1939	GT	TGG
(AGC)	 AG	2088-2180	GT	GGG
(GGC)	 AG	3482-3552	GT	AGG
(GTA)	 AG	3937-4044	GT	AGG
(CGG)	 AG	4222-4390	GT	GAG
-recovered pasa_asmbl_43719.p1, terminal, 4222, 4390
-recovered pasa_asmbl_43719.p1, internal, 1349, 1445
-recovered pasa_asmbl_43719.p1, internal, 1842, 1939
-recovered pasa_asmbl_43719.p1, internal, 2088, 2180
-recovered pasa_asmbl_43719.p1, internal, 3482, 3552
-recovered pasa_asmbl_43719.p1, internal, 3937, 4044
-recovered pasa_asmbl_43719.p1, internal, 4222, 4390
Couldn't classify 376, 785
Couldn't classify 5194, 5324
Sorry, prediction snap_scaffold_489-snap.1-T1 fails validation.
(AAA)	 AG	376-785	GT	ATG
(AGG)	 AG	1349-1445	GT	AGG
(GCC)	 AG	1842-1939	GT	TGG
(AGC)	 AG	2088-2180	GT	GGG
(GGC)	 AG	3482-3552	GT	AGG
(GTA)	 AG	3937-4044	GT	AGG
(CGG)	 AG	4222-4386	GT	ACG
(CTG)	 AG	4464-4477	GT	TGG
(TAT)	 AG	4898-5012	GT	AGG
(ACT)	 AG	5194-5324	GT	AGG
-recovered snap_scaffold_489-snap.1-T1, internal, 376, 785
-recovered snap_scaffold_489-snap.1-T1, internal, 1349, 1445
-recovered snap_scaffold_489-snap.1-T1, internal, 1842, 1939
-recovered snap_scaffold_489-snap.1-T1, internal, 2088, 2180
-recovered snap_scaffold_489-snap.1-T1, internal, 3482, 3552
-recovered snap_scaffold_489-snap.1-T1, internal, 3937, 4044
-recovered snap_scaffold_489-snap.1-T1, internal, 4222, 4386
-recovered snap_scaffold_489-snap.1-T1, internal, 4464, 4477
-recovered snap_scaffold_489-snap.1-T1, internal, 4898, 5012
-recovered snap_scaffold_489-snap.1-T1, internal, 5194, 5324

-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.107775_t
Valid prediction for GeneMark_model.107772_t
Valid prediction for GeneMark_model.107774_t

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

-building trellis in range 1 - 6539
-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 1 predictions from path traversal
GOT 5prime partial gene.

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