-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_339

-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.107353_t
Valid prediction for GeneMark_model.107351_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: -)Couldn't classify 7490, 7702
Sorry, prediction pasa_asmbl_40951.p1 fails validation.
(ATG)	 AC	5388-5537	GT	AGG
(GTG)	 AG	7490-7702	AG	TGA
-recovered pasa_asmbl_40951.p1, initial, 5388, 5537
Valid prediction for HiQ_model.g41030.t1
Valid prediction for GeneMark_model.107350_t
Valid prediction for GlimmerHMM_glimmerT_61728-T1
Couldn't classify 7490, 7699
Sorry, prediction snap_scaffold_339-snap.1-T1 fails validation.
(ATG)	 GT	3035-3338	GT	AGG
(GTA)	 AG	5368-5537	GT	AGG
(GTG)	 AG	7490-7699	GT	TGG
-recovered snap_scaffold_339-snap.1-T1, initial, 3035, 3338
-recovered snap_scaffold_339-snap.1-T1, internal, 5368, 5537
-recovered snap_scaffold_339-snap.1-T1, internal, 7490, 7699
Couldn't classify 1288, 1313
Sorry, prediction GeneMark_model.107354_t fails validation.
(CCC)	 AG	1288-1313	GT	AAG
(AAG)	 AG	1697-1711	GC	AAG
(GAG)	 AG	1734-1808	GT	CAG
(GTC)	 AG	1856-1865	GT	TGG
(AAG)	 AG	1919-1957	CC	AAC
-recovered GeneMark_model.107354_t, terminal, 1919, 1957
-recovered GeneMark_model.107354_t, internal, 1288, 1313
-recovered GeneMark_model.107354_t, internal, 1697, 1711
-recovered GeneMark_model.107354_t, internal, 1734, 1808
-recovered GeneMark_model.107354_t, internal, 1856, 1865
Couldn't classify 1356, 1562
Sorry, prediction snap_scaffold_339-snap.2-T1 fails validation.
(ATT)	 AG	1356-1562	GT	GGG
(TAG)	 AG	2654-2757	AA	AGA
-recovered snap_scaffold_339-snap.2-T1, terminal, 2654, 2757
-recovered snap_scaffold_339-snap.2-T1, internal, 1356, 1562
Valid prediction for GeneMark_model.107352_t

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

-building trellis in range 1 - 7998
-exon list size: 67


building trellis

1.4    
2.9    
4.3    
5.8    
7.2    
8.7    
10.1    
11.6    
13.0    
14.5    
15.9    
17.4    
18.8    
20.3    
21.7    
23.2    
24.6    
26.1    
27.5    
29.0    
30.4    
31.9    
33.3    
34.8    
36.2    
37.7    
39.1    
40.6    
42.0    
43.5    
44.9    
46.4    
47.8    
49.3    
50.7    
52.2    
53.6    
55.1    
56.5    
58.0    
59.4    
60.9    
62.3    
63.8    
65.2    
66.7    
68.1    
69.6    
71.0    
72.5    
73.9    
75.4    
76.8    
78.3    
79.7    
81.2    
82.6    
84.1    
85.5    
87.0    
88.4    
89.9    
91.3    
92.8    
94.2    
95.7    
97.1    
98.6    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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