-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_702

-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: +)
-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 43, 195
Sorry, prediction GeneMark_model.108227_t fails validation.
(AGA)	 AG	43-195	GT	CTG
(GAG)	 AG	285-350	GT	GAG
(AAA)	 AG	389-394	GT	GGG
(GGA)	 AG	421-426	GT	GAG
(GGG)	 AG	448-504	GT	GGG
(CGG)	 AG	538-555	GT	GAG
(GGA)	 AG	2276-2362	GC	GAG
(ATG)	 AG	2395-2643	GC	GAG
(AAG)	 AG	2676-2807	GT	GAG
(AGA)	 AG	2832-2879	GT	AAG
(ATT)	 AG	2907-3095	GT	GAG
(ATG)	 AG	3123-3329	GT	AAG
(AGA)	 AG	3353-3448	GT	GAG
(GGA)	 AG	3469-3585	GT	ATG
(ATG)	 AG	3608-3827	CA	AAC
add_exon() Sorry, GeneMark_model.108227_t 2395-2643-initial-1 is invalid.
-recovered GeneMark_model.108227_t, initial, 2395, 2643
-recovered GeneMark_model.108227_t, initial, 3123, 3329
add_exon() Sorry, GeneMark_model.108227_t 2395-2643-terminal-1 is invalid.
-recovered GeneMark_model.108227_t, terminal, 2395, 2643
-recovered GeneMark_model.108227_t, terminal, 3608, 3827
-recovered GeneMark_model.108227_t, internal, 43, 195
-recovered GeneMark_model.108227_t, internal, 285, 350
-recovered GeneMark_model.108227_t, internal, 389, 394
-recovered GeneMark_model.108227_t, internal, 421, 426
-recovered GeneMark_model.108227_t, internal, 448, 504
-recovered GeneMark_model.108227_t, internal, 538, 555
-recovered GeneMark_model.108227_t, internal, 2276, 2362
-recovered GeneMark_model.108227_t, internal, 2395, 2643
-recovered GeneMark_model.108227_t, internal, 2676, 2807
-recovered GeneMark_model.108227_t, internal, 2832, 2879
-recovered GeneMark_model.108227_t, internal, 2907, 3095
-recovered GeneMark_model.108227_t, internal, 3123, 3329
-recovered GeneMark_model.108227_t, internal, 3353, 3448
-recovered GeneMark_model.108227_t, internal, 3469, 3585
Valid prediction for snap_scaffold_702-snap.2-T1
Couldn't classify 3954, 4083
Sorry, prediction snap_scaffold_702-snap.1-T1 fails validation.
(ATG)	 AG	3075-3448	GT	GAG
(CGG)	 AG	3954-4083	GT	AGG
-recovered snap_scaffold_702-snap.1-T1, initial, 3075, 3448
-recovered snap_scaffold_702-snap.1-T1, internal, 3075, 3448
-recovered snap_scaffold_702-snap.1-T1, internal, 3954, 4083
Valid prediction for GlimmerHMM_glimmerT_62139-T1

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

-building trellis in range 1 - 4935
-exon list size: 39


building trellis

2.4    
4.9    
7.3    
9.8    
12.2    
14.6    
17.1    
19.5    
22.0    
24.4    
26.8    
29.3    
31.7    
34.1    
36.6    
39.0    
41.5    
43.9    
46.3    
48.8    
51.2    
53.7    
56.1    
58.5    
61.0    
63.4    
65.9    
68.3    
70.7    
73.2    
75.6    
78.0    
80.5    
82.9    
85.4    
87.8    
90.2    
92.7    
95.1    
97.6    
-found 2 predictions from path traversal

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