-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_3769647-4099859

-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 snap_scaffold_1-snap.588-T1
Valid prediction for GlimmerHMM_glimmerT_448-T1
Valid prediction for snap_scaffold_1-snap.580-T1
Valid prediction for Augustus_model.g368.t1
Valid prediction for GlimmerHMM_glimmerT_457-T1
Valid prediction for GlimmerHMM_glimmerT_445-T1
Valid prediction for GlimmerHMM_glimmerT_440-T1
Valid prediction for Augustus_model.g371.t1
Valid prediction for GlimmerHMM_glimmerT_466-T1
Valid prediction for snap_scaffold_1-snap.585-T1
Valid prediction for snap_scaffold_1-snap.572-T1
Couldn't classify 324867, 325223
Sorry, prediction pasa_asmbl_1633.p1 fails validation.
(CAA)	 GT	324867-325223	GC	GAG
Valid prediction for snap_scaffold_1-snap.575-T1
Valid prediction for Augustus_model.g367.t1
Valid prediction for snap_scaffold_1-snap.589-T1
Valid prediction for snap_scaffold_1-snap.579-T1
Valid prediction for Augustus_model.g366.t1
Valid prediction for snap_scaffold_1-snap.584-T1
Valid prediction for snap_scaffold_1-snap.563-T1
Valid prediction for GlimmerHMM_glimmerT_453-T1
Valid prediction for snap_scaffold_1-snap.570-T1
Valid prediction for snap_scaffold_1-snap.561-T1
Valid prediction for snap_scaffold_1-snap.574-T1
Valid prediction for snap_scaffold_1-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_450-T1
Valid prediction for snap_scaffold_1-snap.577-T1
Valid prediction for GlimmerHMM_glimmerT_468-T1
Valid prediction for GlimmerHMM_glimmerT_465-T1
Valid prediction for GlimmerHMM_glimmerT_449-T1
Valid prediction for Augustus_model.g377.t1
Valid prediction for snap_scaffold_1-snap.573-T1
Valid prediction for GlimmerHMM_glimmerT_459-T1
Valid prediction for snap_scaffold_1-snap.571-T1
Valid prediction for snap_scaffold_1-snap.586-T1
Valid prediction for snap_scaffold_1-snap.576-T1
Couldn't classify 325377, 325554
Couldn't classify 326969, 327144
Sorry, prediction pasa_asmbl_1634.p1 fails validation.
(CTG)	 CG	325377-325554	GT	AGG
(ACT)	 AG	326969-327144	CT	ACC
Valid prediction for Augustus_model.g376.t1
Valid prediction for snap_scaffold_1-snap.565-T1
Valid prediction for GlimmerHMM_glimmerT_458-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 snap_scaffold_1-snap.568-T1
Valid prediction for CodingQuarry_transcript_2581-T1
Valid prediction for GlimmerHMM_glimmerT_443-T1
Valid prediction for CodingQuarry_transcript_2583-T1
Valid prediction for Augustus_model.g372.t1
Valid prediction for GlimmerHMM_glimmerT_464-T1
Valid prediction for snap_scaffold_1-snap.566-T1
Valid prediction for Augustus_model.g375.t1
Valid prediction for HiQ_model.g373.t1
Valid prediction for GlimmerHMM_glimmerT_455-T1
Valid prediction for snap_scaffold_1-snap.587-T1
Valid prediction for snap_scaffold_1-snap.581-T1
Valid prediction for GlimmerHMM_glimmerT_463-T1
Couldn't classify 67454, 67502
Sorry, prediction pasa_asmbl_178.p1 fails validation.
(GAA)	 AC	67454-67502	GT	AGG
(AGA)	 AG	68846-68942	GT	CGG
(GTT)	 AG	70166-70246	GT	AGG
(CGA)	 AG	72029-72083	GT	AGG
(CAA)	 AG	73332-73490	CC	AGC
-recovered pasa_asmbl_178.p1, terminal, 73332, 73490
-recovered pasa_asmbl_178.p1, internal, 68846, 68942
-recovered pasa_asmbl_178.p1, internal, 70166, 70246
-recovered pasa_asmbl_178.p1, internal, 72029, 72083
Valid prediction for snap_scaffold_1-snap.562-T1
Valid prediction for snap_scaffold_1-snap.578-T1
Valid prediction for Augustus_model.g379.t1
Valid prediction for GlimmerHMM_glimmerT_442-T1
Valid prediction for Augustus_model.g374.t1
Valid prediction for GlimmerHMM_glimmerT_444-T1
Valid prediction for snap_scaffold_1-snap.569-T1
Valid prediction for GlimmerHMM_glimmerT_451-T1
Valid prediction for CodingQuarry_transcript_2582-T1
Valid prediction for GlimmerHMM_glimmerT_452-T1
Valid prediction for GlimmerHMM_glimmerT_454-T1
Valid prediction for pasa_asmbl_175.p1
Valid prediction for snap_scaffold_1-snap.560-T1
Valid prediction for GlimmerHMM_glimmerT_467-T1
Valid prediction for snap_scaffold_1-snap.564-T1
Valid prediction for GlimmerHMM_glimmerT_461-T1
Valid prediction for Augustus_model.g370.t1
Valid prediction for Augustus_model.g378.t1
Valid prediction for GlimmerHMM_glimmerT_447-T1
Valid prediction for GlimmerHMM_glimmerT_460-T1
Valid prediction for Augustus_model.g369.t1
Valid prediction for snap_scaffold_1-snap.567-T1
Valid prediction for GlimmerHMM_glimmerT_441-T1
Valid prediction for GlimmerHMM_glimmerT_446-T1
Valid prediction for snap_scaffold_1-snap.582-T1
Valid prediction for GlimmerHMM_glimmerT_456-T1
Valid prediction for GlimmerHMM_glimmerT_462-T1

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

-building trellis in range 1 - 330213
-exon list size: 228


building trellis

0.4    
0.9    
1.3    
1.7    
2.2    
2.6    
3.0    
3.5    
3.9    
4.3    
4.8    
5.2    
5.7    
6.1    
6.5    
7.0    
7.4    
7.8    
8.3    
8.7    
9.1    
9.6    
10.0    
10.4    
10.9    
11.3    
11.7    
12.2    
12.6    
13.0    
13.5    
13.9    
14.3    
14.8    
15.2    
15.7    
16.1    
16.5    
17.0    
17.4    
17.8    
18.3    
18.7    
19.1    
19.6    
20.0    
20.4    
20.9    
21.3    
21.7    
22.2    
22.6    
23.0    
23.5    
23.9    
24.3    
24.8    
25.2    
25.7    
26.1    
26.5    
27.0    
27.4    
27.8    
28.3    
28.7    
29.1    
29.6    
30.0    
30.4    
30.9    
31.3    
31.7    
32.2    
32.6    
33.0    
33.5    
33.9    
34.3    
34.8    
35.2    
35.7    
36.1    
36.5    
37.0    
37.4    
37.8    
38.3    
38.7    
39.1    
39.6    
40.0    
40.4    
40.9    
41.3    
41.7    
42.2    
42.6    
43.0    
43.5    
43.9    
44.3    
44.8    
45.2    
45.7    
46.1    
46.5    
47.0    
47.4    
47.8    
48.3    
48.7    
49.1    
49.6    
50.0    
50.4    
50.9    
51.3    
51.7    
52.2    
52.6    
53.0    
53.5    
53.9    
54.3    
54.8    
55.2    
55.7    
56.1    
56.5    
57.0    
57.4    
57.8    
58.3    
58.7    
59.1    
59.6    
60.0    
60.4    
60.9    
61.3    
61.7    
62.2    
62.6    
63.0    
63.5    
63.9    
64.3    
64.8    
65.2    
65.7    
66.1    
66.5    
67.0    
67.4    
67.8    
68.3    
68.7    
69.1    
69.6    
70.0    
70.4    
70.9    
71.3    
71.7    
72.2    
72.6    
73.0    
73.5    
73.9    
74.3    
74.8    
75.2    
75.7    
76.1    
76.5    
77.0    
77.4    
77.8    
78.3    
78.7    
79.1    
79.6    
80.0    
80.4    
80.9    
81.3    
81.7    
82.2    
82.6    
83.0    
83.5    
83.9    
84.3    
84.8    
85.2    
85.7    
86.1    
86.5    
87.0    
87.4    
87.8    
88.3    
88.7    
89.1    
89.6    
90.0    
90.4    
90.9    
91.3    
91.7    
92.2    
92.6    
93.0    
93.5    
93.9    
94.3    
94.8    
95.2    
95.7    
96.1    
96.5    
97.0    
97.4    
97.8    
98.3    
98.7    
99.1    
99.6    
-found 31 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10297
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support