-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_567

-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 GeneMark_model.107947_t
Couldn't classify 5115, 5163
Sorry, prediction GeneMark_model.107948_t fails validation.
(ATG)	 TG	2801-3019	GT	GGG
(GTT)	 AG	3111-3142	GT	GAG
(GAG)	 AG	3173-3256	GC	GGG
(AAG)	 AG	3280-3288	GC	GAG
(GCA)	 AG	3311-3316	GT	ATG
(AGT)	 AG	3354-3419	GT	GAG
(AAA)	 AG	3453-3599	GT	GGG
(ACA)	 AG	4335-4454	GT	AGG
(GAA)	 AG	4480-4500	GT	GAG
(TGG)	 AG	4525-4542	GT	GAG
(TGT)	 AG	4579-4590	GT	GGG
(GAA)	 AG	4612-4776	GT	GAG
(ACA)	 AG	4802-4927	GT	GAG
(AGA)	 AG	4955-5086	GT	GAG
(CAA)	 AG	5115-5163	GT	ATG
-recovered GeneMark_model.107948_t, initial, 2801, 3019
add_exon() Sorry, GeneMark_model.107948_t 3111-3142-terminal-2 is invalid.
-recovered GeneMark_model.107948_t, terminal, 3111, 3142
-recovered GeneMark_model.107948_t, terminal, 4480, 4500
-recovered GeneMark_model.107948_t, internal, 3111, 3142
-recovered GeneMark_model.107948_t, internal, 3173, 3256
-recovered GeneMark_model.107948_t, internal, 3280, 3288
-recovered GeneMark_model.107948_t, internal, 3311, 3316
-recovered GeneMark_model.107948_t, internal, 3354, 3419
-recovered GeneMark_model.107948_t, internal, 3453, 3599
-recovered GeneMark_model.107948_t, internal, 4335, 4454
-recovered GeneMark_model.107948_t, internal, 4480, 4500
-recovered GeneMark_model.107948_t, internal, 4525, 4542
-recovered GeneMark_model.107948_t, internal, 4579, 4590
-recovered GeneMark_model.107948_t, internal, 4612, 4776
-recovered GeneMark_model.107948_t, internal, 4802, 4927
-recovered GeneMark_model.107948_t, internal, 4955, 5086
-recovered GeneMark_model.107948_t, internal, 5115, 5163
Valid prediction for GlimmerHMM_glimmerT_62000-T1

-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 5667, 5735
Sorry, prediction GeneMark_model.107946_t fails validation.
(ATG)	 AG	5237-5253	GT	ATG
(AGG)	 AG	5309-5440	GT	GAG
(GAA)	 AG	5667-5735	GC	GGG
-recovered GeneMark_model.107946_t, initial, 5237, 5253
-recovered GeneMark_model.107946_t, internal, 5237, 5253
-recovered GeneMark_model.107946_t, internal, 5309, 5440
-recovered GeneMark_model.107946_t, internal, 5667, 5735
Valid prediction for GlimmerHMM_glimmerT_61999-T1
Couldn't classify 1395, 1487
Sorry, prediction snap_scaffold_567-snap.1-T1 fails validation.
(AGT)	 AG	1395-1487	GT	AGG
(AAT)	 AG	2669-2971	GT	CGG
(TCA)	 AG	4772-4818	GT	AGG
(ACC)	 AG	5292-5444	AA	AAA
-recovered snap_scaffold_567-snap.1-T1, terminal, 5292, 5444
-recovered snap_scaffold_567-snap.1-T1, internal, 1395, 1487
-recovered snap_scaffold_567-snap.1-T1, internal, 2669, 2971
-recovered snap_scaffold_567-snap.1-T1, internal, 4772, 4818
Valid prediction for Augustus_model.g41210.t1

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

-building trellis in range 1 - 5766
-exon list size: 59


building trellis

1.6    
3.3    
4.9    
6.6    
8.2    
9.8    
11.5    
13.1    
14.8    
16.4    
18.0    
19.7    
21.3    
23.0    
24.6    
26.2    
27.9    
29.5    
31.1    
32.8    
34.4    
36.1    
37.7    
39.3    
41.0    
42.6    
44.3    
45.9    
47.5    
49.2    
50.8    
52.5    
54.1    
55.7    
57.4    
59.0    
60.7    
62.3    
63.9    
65.6    
67.2    
68.9    
70.5    
72.1    
73.8    
75.4    
77.0    
78.7    
80.3    
82.0    
83.6    
85.2    
86.9    
88.5    
90.2    
91.8    
93.4    
95.1    
96.7    
98.4    
-found 2 predictions from path traversal

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