-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_55

-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_61089-T1
Valid prediction for GlimmerHMM_glimmerT_61082-T1
Valid prediction for GlimmerHMM_glimmerT_61083-T1
Valid prediction for snap_scaffold_55-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_61086-T1
Valid prediction for Augustus_model.g40642.t1
Valid prediction for GeneMark_model.106293_t
Valid prediction for GlimmerHMM_glimmerT_61084-T1
Valid prediction for GlimmerHMM_glimmerT_61093-T1
Valid prediction for snap_scaffold_55-snap.5-T1
Valid prediction for Augustus_model.g40638.t1
Valid prediction for GeneMark_model.106298_t
Valid prediction for snap_scaffold_55-snap.6-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_55-snap.4-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g40637.t1
Valid prediction for GlimmerHMM_glimmerT_61085-T1
Valid prediction for Augustus_model.g40636.t1
Valid prediction for snap_scaffold_55-snap.2-T1
Valid prediction for snap_scaffold_55-snap.3-T1
Valid prediction for Augustus_model.g40635.t1
Valid prediction for snap_scaffold_55-snap.1-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_55-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_61088-T1
Valid prediction for Augustus_model.g40639.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 GeneMark_model.106303_t
Couldn't classify 312, 450
Sorry, prediction GeneMark_model.106305_t fails validation.
(CTG)	 AG	312-450	GT	CAG
(GAA)	 AG	801-876	GT	AGG
(GTG)	 AG	1001-1105	GT	CTG
(GCT)	 AG	1406-1438	GT	CTG
(GCG)	 AG	1699-1704	GG	AAG
-recovered GeneMark_model.106305_t, terminal, 1699, 1704
-recovered GeneMark_model.106305_t, internal, 312, 450
-recovered GeneMark_model.106305_t, internal, 801, 876
-recovered GeneMark_model.106305_t, internal, 1001, 1105
-recovered GeneMark_model.106305_t, internal, 1406, 1438
Valid prediction for GlimmerHMM_glimmerT_61091-T1
Couldn't classify 312, 443
Sorry, prediction GlimmerHMM_glimmerT_61094-T1 fails validation.
(CTG)	 AG	312-443	GT	AGG
(TTT)	 AG	785-876	GT	AGG
(GTG)	 AG	1001-1105	GT	CTG
(GAA)	 AG	1204-1276	GT	AGG
(GCT)	 AG	1406-1535	GT	AAG
(GCG)	 AG	1699-1754	GT	CTG
(CAA)	 AG	2917-3056	TA	GAT
-recovered GlimmerHMM_glimmerT_61094-T1, terminal, 2917, 3056
-recovered GlimmerHMM_glimmerT_61094-T1, internal, 312, 443
-recovered GlimmerHMM_glimmerT_61094-T1, internal, 785, 876
-recovered GlimmerHMM_glimmerT_61094-T1, internal, 1001, 1105
-recovered GlimmerHMM_glimmerT_61094-T1, internal, 1204, 1276
-recovered GlimmerHMM_glimmerT_61094-T1, internal, 1406, 1535
-recovered GlimmerHMM_glimmerT_61094-T1, internal, 1699, 1754
Valid prediction for GlimmerHMM_glimmerT_61092-T1
Valid prediction for GeneMark_model.106302_t
Valid prediction for Augustus_model.g40641.t1
Valid prediction for GlimmerHMM_glimmerT_61087-T1
Valid prediction for Augustus_model.g40643.t1
Valid prediction for snap_scaffold_55-snap.8-T1
Valid prediction for GeneMark_model.106299_t
Valid prediction for Augustus_model.g40640.t1
Valid prediction for snap_scaffold_55-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_61090-T1

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

-building trellis in range 1 - 26217
-exon list size: 108


building trellis

0.9    
1.8    
2.7    
3.6    
4.5    
5.5    
6.4    
7.3    
8.2    
9.1    
10.0    
10.9    
11.8    
12.7    
13.6    
14.5    
15.5    
16.4    
17.3    
18.2    
19.1    
20.0    
20.9    
21.8    
22.7    
23.6    
24.5    
25.5    
26.4    
27.3    
28.2    
29.1    
30.0    
30.9    
31.8    
32.7    
33.6    
34.5    
35.5    
36.4    
37.3    
38.2    
39.1    
40.0    
40.9    
41.8    
42.7    
43.6    
44.5    
45.5    
46.4    
47.3    
48.2    
49.1    
50.0    
50.9    
51.8    
52.7    
53.6    
54.5    
55.5    
56.4    
57.3    
58.2    
59.1    
60.0    
60.9    
61.8    
62.7    
63.6    
64.5    
65.5    
66.4    
67.3    
68.2    
69.1    
70.0    
70.9    
71.8    
72.7    
73.6    
74.5    
75.5    
76.4    
77.3    
78.2    
79.1    
80.0    
80.9    
81.8    
82.7    
83.6    
84.5    
85.5    
86.4    
87.3    
88.2    
89.1    
90.0    
90.9    
91.8    
92.7    
93.6    
94.5    
95.5    
96.4    
97.3    
98.2    
99.1    
-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