-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_35

-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 GlimmerHMM_glimmerT_59501-T1
Valid prediction for snap_scaffold_35-snap.9-T1
Valid prediction for snap_scaffold_35-snap.7-T1
Valid prediction for snap_scaffold_35-snap.5-T1
Valid prediction for snap_scaffold_35-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_59504-T1
Valid prediction for Augustus_model.g39412.t1
Valid prediction for snap_scaffold_35-snap.8-T1
Valid prediction for GlimmerHMM_glimmerT_59506-T1
Valid prediction for GlimmerHMM_glimmerT_59507-T1
Valid prediction for Augustus_model.g39413.t1
Valid prediction for Augustus_model.g39410.t1
Valid prediction for GlimmerHMM_glimmerT_59508-T1
Couldn't classify 113, 225
Sorry, prediction Augustus_model.g39408.t1 fails validation.
(GTT)	 AG	113-225	GT	AGG
(ATT)	 AG	398-547	GT	AGG
(AGA)	 AG	743-853	GT	CGG
(AGA)	 AG	1345-1485	GT	AGG
(GTG)	 AG	1620-1733	GT	CTG
(GAG)	 AG	1835-1907	GT	AGG
(ACT)	 AG	1989-2127	GT	AAG
(GTG)	 AG	2224-2273	GT	CTG
(CGA)	 AG	3902-4041	TA	GAT
-recovered Augustus_model.g39408.t1, terminal, 3902, 4041
-recovered Augustus_model.g39408.t1, internal, 113, 225
-recovered Augustus_model.g39408.t1, internal, 398, 547
-recovered Augustus_model.g39408.t1, internal, 743, 853
-recovered Augustus_model.g39408.t1, internal, 1345, 1485
-recovered Augustus_model.g39408.t1, internal, 1620, 1733
-recovered Augustus_model.g39408.t1, internal, 1835, 1907
-recovered Augustus_model.g39408.t1, internal, 1989, 2127
-recovered Augustus_model.g39408.t1, internal, 2224, 2273
Couldn't classify 113, 225
Sorry, prediction snap_scaffold_35-snap.1-T1 fails validation.
(GTT)	 AG	113-225	GT	AGG
(ATT)	 AG	398-547	GT	AGG
(AGA)	 AG	743-868	TT	GAT
-recovered snap_scaffold_35-snap.1-T1, terminal, 743, 868
-recovered snap_scaffold_35-snap.1-T1, internal, 113, 225
-recovered snap_scaffold_35-snap.1-T1, internal, 398, 547

-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 snap_scaffold_35-snap.14-T1
Valid prediction for GlimmerHMM_glimmerT_59505-T1
Valid prediction for snap_scaffold_35-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_59503-T1
Valid prediction for snap_scaffold_35-snap.13-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g39411.t1
Valid prediction for Augustus_model.g39415.t1
Valid prediction for GlimmerHMM_glimmerT_59509-T1
Valid prediction for Augustus_model.g39414.t1
Valid prediction for snap_scaffold_35-snap.11-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_35-snap.6-T1
Valid prediction for snap_scaffold_35-snap.4-T1
Valid prediction for Augustus_model.g39409.t1
Valid prediction for GlimmerHMM_glimmerT_59511-T1
Valid prediction for Augustus_model.g39416.t1
Couldn't classify 7949, 8305
Sorry, prediction pasa_asmbl_41030.p1 fails validation.
(AAA)	 GC	7949-8305	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_59502-T1
Valid prediction for snap_scaffold_35-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_59510-T1
Valid prediction for snap_scaffold_35-snap.12-T1

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

-building trellis in range 1 - 39404
-exon list size: 91


building trellis

1.1    
2.2    
3.2    
4.3    
5.4    
6.5    
7.5    
8.6    
9.7    
10.8    
11.8    
12.9    
14.0    
15.1    
16.1    
17.2    
18.3    
19.4    
20.4    
21.5    
22.6    
23.7    
24.7    
25.8    
26.9    
28.0    
29.0    
30.1    
31.2    
32.3    
33.3    
34.4    
35.5    
36.6    
37.6    
38.7    
39.8    
40.9    
41.9    
43.0    
44.1    
45.2    
46.2    
47.3    
48.4    
49.5    
50.5    
51.6    
52.7    
53.8    
54.8    
55.9    
57.0    
58.1    
59.1    
60.2    
61.3    
62.4    
63.4    
64.5    
65.6    
66.7    
67.7    
68.8    
69.9    
71.0    
72.0    
73.1    
74.2    
75.3    
76.3    
77.4    
78.5    
79.6    
80.6    
81.7    
82.8    
83.9    
84.9    
86.0    
87.1    
88.2    
89.2    
90.3    
91.4    
92.5    
93.5    
94.6    
95.7    
96.8    
97.8    
98.9    
-found 12 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support