-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_394

-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 7006, 7026
Sorry, prediction GeneMark_model.107511_t fails validation.
(ATG)	 GT	6160-6179	GT	GGG
(AGA)	 AG	6405-6464	GT	GAG
(GGA)	 AG	6505-6555	GT	GGG
(AGG)	 AG	6583-6621	GT	GTG
(GAG)	 AG	6650-6664	GT	GAG
(AGA)	 AG	6687-6698	GT	AGG
(AGA)	 AG	7006-7026	GT	GAG
-recovered GeneMark_model.107511_t, initial, 6160, 6179
-recovered GeneMark_model.107511_t, internal, 6405, 6464
-recovered GeneMark_model.107511_t, internal, 6505, 6555
-recovered GeneMark_model.107511_t, internal, 6583, 6621
-recovered GeneMark_model.107511_t, internal, 6650, 6664
-recovered GeneMark_model.107511_t, internal, 6687, 6698
-recovered GeneMark_model.107511_t, internal, 7006, 7026
Valid prediction for GlimmerHMM_glimmerT_61791-T1
Valid prediction for GeneMark_model.107509_t

-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 GlimmerHMM_glimmerT_61790-T1
Valid prediction for GeneMark_model.107510_t
Couldn't classify 3571, 3889
Sorry, prediction snap_scaffold_394-snap.1-T1 fails validation.
(TCC)	 AG	3571-3889	GT	CAG
(GGA)	 AG	4427-4741	GT	TAG
(ACT)	 AG	5580-5732	GT	CAG
(TAT)	 AG	5912-5981	GT	TGG
(GTG)	 AG	5998-6197	TA	GAT
-recovered snap_scaffold_394-snap.1-T1, terminal, 5998, 6197
-recovered snap_scaffold_394-snap.1-T1, internal, 3571, 3889
-recovered snap_scaffold_394-snap.1-T1, internal, 4427, 4741
-recovered snap_scaffold_394-snap.1-T1, internal, 5580, 5732
-recovered snap_scaffold_394-snap.1-T1, internal, 5912, 5981
Valid prediction for Augustus_model.g41066.t1
Couldn't classify 7285, 7341
Sorry, prediction GeneMark_model.107508_t fails validation.
(ATG)	 AA	5803-5880	GT	TTG
(TAT)	 AG	5912-5945	GT	TAG
(GTG)	 AG	5998-6034	GT	GAG
(AGG)	 AG	6061-6129	GT	AGG
(GAA)	 AG	6885-6905	GT	GAG
(AGC)	 AG	7253-7261	GT	GAG
(AGA)	 AG	7285-7341	GC	GAG
-recovered GeneMark_model.107508_t, initial, 5803, 5880
add_exon() Sorry, GeneMark_model.107508_t 5998-6034-terminal-3 is invalid.
-recovered GeneMark_model.107508_t, terminal, 5998, 6034
-recovered GeneMark_model.107508_t, internal, 5912, 5945
-recovered GeneMark_model.107508_t, internal, 5998, 6034
-recovered GeneMark_model.107508_t, internal, 6061, 6129
-recovered GeneMark_model.107508_t, internal, 6885, 6905
-recovered GeneMark_model.107508_t, internal, 7253, 7261
-recovered GeneMark_model.107508_t, internal, 7285, 7341

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

-building trellis in range 1 - 7370
-exon list size: 52


building trellis

1.9    
3.7    
5.6    
7.4    
9.3    
11.1    
13.0    
14.8    
16.7    
18.5    
20.4    
22.2    
24.1    
25.9    
27.8    
29.6    
31.5    
33.3    
35.2    
37.0    
38.9    
40.7    
42.6    
44.4    
46.3    
48.1    
50.0    
51.9    
53.7    
55.6    
57.4    
59.3    
61.1    
63.0    
64.8    
66.7    
68.5    
70.4    
72.2    
74.1    
75.9    
77.8    
79.6    
81.5    
83.3    
85.2    
87.0    
88.9    
90.7    
92.6    
94.4    
96.3    
98.1    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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