-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_3651969-3713382

-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_52318-T1
Valid prediction for snap_scaffold_24-snap.806-T1
Valid prediction for snap_scaffold_24-snap.804-T1
Valid prediction for pasa_asmbl_32157.p1
Valid prediction for snap_scaffold_24-snap.805-T1
Valid prediction for GlimmerHMM_glimmerT_52316-T1
Valid prediction for snap_scaffold_24-snap.810-T1
Valid prediction for Augustus_model.g34845.t1
Valid prediction for snap_scaffold_24-snap.809-T1
Valid prediction for GlimmerHMM_glimmerT_52320-T1
Valid prediction for snap_scaffold_24-snap.807-T1
Valid prediction for HiQ_model.g34846.t1
Valid prediction for snap_scaffold_24-snap.802-T1
Valid prediction for snap_scaffold_24-snap.811-T1
Valid prediction for CodingQuarry_transcript_37280-T1
Valid prediction for GlimmerHMM_glimmerT_52311-T1
Valid prediction for Augustus_model.g34844.t1
Valid prediction for GlimmerHMM_glimmerT_52319-T1
Valid prediction for HiQ_model.g34839.t1
Valid prediction for GlimmerHMM_glimmerT_52314-T1
Valid prediction for Augustus_model.g34841.t1
Valid prediction for HiQ_model.g34837.t1
Valid prediction for Augustus_model.g34843.t1
Valid prediction for GlimmerHMM_glimmerT_52315-T1
Valid prediction for pasa_asmbl_32155.p1
Valid prediction for GlimmerHMM_glimmerT_52321-T1
Valid prediction for snap_scaffold_24-snap.803-T1
Valid prediction for GlimmerHMM_glimmerT_52313-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: -)Valid prediction for GlimmerHMM_glimmerT_52317-T1
Valid prediction for GlimmerHMM_glimmerT_52310-T1
Valid prediction for snap_scaffold_24-snap.801-T1
Valid prediction for Augustus_model.g34840.t1
Valid prediction for CodingQuarry_transcript_37279-T1
Valid prediction for Augustus_model.g34838.t1
Couldn't classify 54394, 54451
Sorry, prediction pasa_asmbl_32835.p1 fails validation.
(ACT)	 CC	54394-54451	GT	TGG
(CTT)	 AG	54607-54672	GT	AGG
(ATC)	 AG	55141-55241	GT	AGG
(GGA)	 AG	55596-55721	GT	GGG
(AAT)	 AG	56110-56176	GT	AGG
(ATA)	 AG	56287-56367	GT	AGG
(TCC)	 AG	56462-56502	GA	AAG
add_exon() Sorry, pasa_asmbl_32835.p1 56110-56176-terminal-3 is invalid.
-recovered pasa_asmbl_32835.p1, terminal, 56110, 56176
-recovered pasa_asmbl_32835.p1, terminal, 56462, 56502
-recovered pasa_asmbl_32835.p1, internal, 54607, 54672
-recovered pasa_asmbl_32835.p1, internal, 55141, 55241
-recovered pasa_asmbl_32835.p1, internal, 55596, 55721
-recovered pasa_asmbl_32835.p1, internal, 56110, 56176
-recovered pasa_asmbl_32835.p1, internal, 56287, 56367
Valid prediction for snap_scaffold_24-snap.808-T1
Valid prediction for Augustus_model.g34847.t1
Valid prediction for Augustus_model.g34842.t1
Valid prediction for snap_scaffold_24-snap.800-T1
Valid prediction for GlimmerHMM_glimmerT_52322-T1
Valid prediction for GlimmerHMM_glimmerT_52309-T1
Valid prediction for GlimmerHMM_glimmerT_52312-T1

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

-building trellis in range 1 - 61414
-exon list size: 102


building trellis

1.0    
1.9    
2.9    
3.8    
4.8    
5.8    
6.7    
7.7    
8.7    
9.6    
10.6    
11.5    
12.5    
13.5    
14.4    
15.4    
16.3    
17.3    
18.3    
19.2    
20.2    
21.2    
22.1    
23.1    
24.0    
25.0    
26.0    
26.9    
27.9    
28.8    
29.8    
30.8    
31.7    
32.7    
33.7    
34.6    
35.6    
36.5    
37.5    
38.5    
39.4    
40.4    
41.3    
42.3    
43.3    
44.2    
45.2    
46.2    
47.1    
48.1    
49.0    
50.0    
51.0    
51.9    
52.9    
53.8    
54.8    
55.8    
56.7    
57.7    
58.7    
59.6    
60.6    
61.5    
62.5    
63.5    
64.4    
65.4    
66.3    
67.3    
68.3    
69.2    
70.2    
71.2    
72.1    
73.1    
74.0    
75.0    
76.0    
76.9    
77.9    
78.8    
79.8    
80.8    
81.7    
82.7    
83.7    
84.6    
85.6    
86.5    
87.5    
88.5    
89.4    
90.4    
91.3    
92.3    
93.3    
94.2    
95.2    
96.2    
97.1    
98.1    
99.0    
-found 14 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support