-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_657

-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 4847, 4901
Sorry, prediction GeneMark_model.108145_t fails validation.
(ATG)	 AC	3414-3478	GT	GGG
(AAA)	 AG	3701-3706	GT	ATG
(GGA)	 AG	3750-3770	GT	ATG
(GGA)	 AG	3870-3896	GT	GAG
(ACA)	 AG	3918-4127	GT	AGG
(AGG)	 AG	4847-4901	GT	CTG
-recovered GeneMark_model.108145_t, initial, 3414, 3478
-recovered GeneMark_model.108145_t, internal, 3701, 3706
-recovered GeneMark_model.108145_t, internal, 3750, 3770
-recovered GeneMark_model.108145_t, internal, 3870, 3896
-recovered GeneMark_model.108145_t, internal, 3918, 4127
-recovered GeneMark_model.108145_t, internal, 4847, 4901
Couldn't classify 4416, 4641
Sorry, prediction GlimmerHMM_glimmerT_62096-T1 fails validation.
(ATG)	 AC	3414-3486	GT	GTG
(ACG)	 AG	4416-4641	GT	CTG
-recovered GlimmerHMM_glimmerT_62096-T1, initial, 3414, 3486
-recovered GlimmerHMM_glimmerT_62096-T1, internal, 4416, 4641
Couldn't classify 1310, 1407
Sorry, prediction snap_scaffold_657-snap.1-T1 fails validation.
(ATT)	 AG	1310-1407	GT	ATG
(GAA)	 AG	1837-1913	GT	AGG
(GAG)	 AG	2616-2712	CA	AAC
-recovered snap_scaffold_657-snap.1-T1, terminal, 2616, 2712
-recovered snap_scaffold_657-snap.1-T1, internal, 1310, 1407
-recovered snap_scaffold_657-snap.1-T1, internal, 1837, 1913

-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: -)Couldn't classify 4833, 4948
Sorry, prediction GeneMark_model.108144_t fails validation.
(ATG)	 CG	3215-3223	GT	AGG
(GGG)	 AG	4331-4407	GT	CTG
(GGT)	 AG	4445-4450	GT	GTG
(GGG)	 AG	4485-4526	GT	GAG
(GAC)	 AG	4833-4948	GT	CGG
-recovered GeneMark_model.108144_t, initial, 3215, 3223
add_exon() Sorry, GeneMark_model.108144_t 4485-4526-terminal-1 is invalid.
-recovered GeneMark_model.108144_t, terminal, 4485, 4526
-recovered GeneMark_model.108144_t, internal, 4331, 4407
-recovered GeneMark_model.108144_t, internal, 4445, 4450
-recovered GeneMark_model.108144_t, internal, 4485, 4526
-recovered GeneMark_model.108144_t, internal, 4833, 4948
Couldn't classify 4833, 4948
Sorry, prediction Augustus_model.g41277.t1 fails validation.
(ATG)	 TG	4645-4673	GT	AGG
(GAC)	 AG	4833-4948	GT	CGG
-recovered Augustus_model.g41277.t1, initial, 4645, 4673
-recovered Augustus_model.g41277.t1, internal, 4833, 4948
Valid prediction for GlimmerHMM_glimmerT_62095-T1

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

-building trellis in range 1 - 5094
-exon list size: 34


building trellis

2.8    
5.6    
8.3    
11.1    
13.9    
16.7    
19.4    
22.2    
25.0    
27.8    
30.6    
33.3    
36.1    
38.9    
41.7    
44.4    
47.2    
50.0    
52.8    
55.6    
58.3    
61.1    
63.9    
66.7    
69.4    
72.2    
75.0    
77.8    
80.6    
83.3    
86.1    
88.9    
91.7    
94.4    
97.2    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support