-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_940

-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 543, 563
Sorry, prediction GeneMark_model.108638_t fails validation.
(GAA)	 AG	543-563	GT	AGG
(GAA)	 AG	625-645	GT	AGG
(GAA)	 AG	707-727	GT	AGG
(GAA)	 AG	789-809	GT	AGG
(GAA)	 AG	871-891	GT	AGG
(GAA)	 AG	953-972	GT	CAG
(ATT)	 AG	1007-1050	GT	AGG
(TCT)	 AG	1413-1547	GT	GAG
(ACA)	 AG	1581-1614	GT	AAG
(GCA)	 AG	1648-1732	AG	AGA
add_exon() Sorry, GeneMark_model.108638_t 1007-1050-terminal-2 is invalid.
-recovered GeneMark_model.108638_t, terminal, 1007, 1050
-recovered GeneMark_model.108638_t, terminal, 1648, 1732
-recovered GeneMark_model.108638_t, internal, 543, 563
-recovered GeneMark_model.108638_t, internal, 625, 645
-recovered GeneMark_model.108638_t, internal, 707, 727
-recovered GeneMark_model.108638_t, internal, 789, 809
-recovered GeneMark_model.108638_t, internal, 871, 891
-recovered GeneMark_model.108638_t, internal, 953, 972
-recovered GeneMark_model.108638_t, internal, 1007, 1050
-recovered GeneMark_model.108638_t, internal, 1413, 1547
-recovered GeneMark_model.108638_t, internal, 1581, 1614
Couldn't classify 97, 226
Couldn't classify 3418, 3490
Sorry, prediction snap_scaffold_940-snap.1-T1 fails validation.
(TCA)	 AG	97-226	GT	AGG
(GAA)	 AG	543-563	GT	AGG
(GAA)	 AG	625-645	GT	AGG
(GAA)	 AG	707-727	GT	AGG
(GAA)	 AG	789-809	GT	AGG
(GAA)	 AG	871-899	GT	GAG
(GAA)	 AG	953-1050	GT	AGG
(TCT)	 AG	1413-1547	GT	GAG
(GCT)	 AG	2287-2335	GT	GGG
(GAA)	 AG	3418-3490	GT	ATG
add_exon() Sorry, snap_scaffold_940-snap.1-T1 953-1050-terminal-2 is invalid.
-recovered snap_scaffold_940-snap.1-T1, terminal, 953, 1050
-recovered snap_scaffold_940-snap.1-T1, internal, 97, 226
-recovered snap_scaffold_940-snap.1-T1, internal, 543, 563
-recovered snap_scaffold_940-snap.1-T1, internal, 625, 645
-recovered snap_scaffold_940-snap.1-T1, internal, 707, 727
-recovered snap_scaffold_940-snap.1-T1, internal, 789, 809
-recovered snap_scaffold_940-snap.1-T1, internal, 871, 899
-recovered snap_scaffold_940-snap.1-T1, internal, 953, 1050
-recovered snap_scaffold_940-snap.1-T1, internal, 1413, 1547
-recovered snap_scaffold_940-snap.1-T1, internal, 2287, 2335
-recovered snap_scaffold_940-snap.1-T1, internal, 3418, 3490
Valid prediction for Augustus_model.g41449.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 35, 67
Sorry, prediction GeneMark_model.108639_t fails validation.
(GGT)	 AG	35-67	GT	GGG
(AGG)	 AG	92-121	GT	GGG
(GGG)	 AG	1315-1435	AT	GAA
-recovered GeneMark_model.108639_t, terminal, 1315, 1435
-recovered GeneMark_model.108639_t, internal, 35, 67
-recovered GeneMark_model.108639_t, internal, 92, 121

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

-building trellis in range 1 - 3902
-exon list size: 42


building trellis

2.3    
4.5    
6.8    
9.1    
11.4    
13.6    
15.9    
18.2    
20.5    
22.7    
25.0    
27.3    
29.5    
31.8    
34.1    
36.4    
38.6    
40.9    
43.2    
45.5    
47.7    
50.0    
52.3    
54.5    
56.8    
59.1    
61.4    
63.6    
65.9    
68.2    
70.5    
72.7    
75.0    
77.3    
79.5    
81.8    
84.1    
86.4    
88.6    
90.9    
93.2    
95.5    
97.7    
-found 2 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

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