-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_39

-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.106204_t
Couldn't classify 35512, 35541
Sorry, prediction GeneMark_model.106209_t fails validation.
(ATG)	 GA	35201-35259	GT	AAG
(GGT)	 AG	35282-35356	GT	TGG
(GGG)	 AG	35512-35541	GT	AGG
-recovered GeneMark_model.106209_t, initial, 35201, 35259
-recovered GeneMark_model.106209_t, internal, 35282, 35356
-recovered GeneMark_model.106209_t, internal, 35512, 35541
Valid prediction for snap_scaffold_39-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_61001-T1
Valid prediction for pasa_asmbl_41027.p1
Valid prediction for GlimmerHMM_glimmerT_61000-T1
Valid prediction for snap_scaffold_39-snap.8-T1
Valid prediction for snap_scaffold_39-snap.2-T1
Valid prediction for snap_scaffold_39-snap.3-T1
Valid prediction for Augustus_model.g40581.t1
Valid prediction for GeneMark_model.106205_t
Valid prediction for CodingQuarry_transcript_46477-T1
Valid prediction for GeneMark_model.106203_t
Valid prediction for Augustus_model.g40580.t1
Valid prediction for GeneMark_model.106207_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: -)Valid prediction for snap_scaffold_39-snap.5-T1
Valid prediction for GeneMark_model.106202_t
Valid prediction for CodingQuarry_transcript_46479-T1
Valid prediction for GlimmerHMM_glimmerT_61002-T1
Valid prediction for GeneMark_model.106206_t
Valid prediction for GlimmerHMM_glimmerT_60997-T1
Valid prediction for GeneMark_model.106208_t
Valid prediction for Augustus_model.g40582.t1
Couldn't classify 35424, 35456
Sorry, prediction snap_scaffold_39-snap.1-T1 fails validation.
(ATG)	 AC	29479-29655	GT	AGG
(TTT)	 AG	30208-30300	GT	AGG
(GTC)	 AG	30635-30791	GT	GAG
(TCC)	 AG	30874-30926	GT	TGG
(TTT)	 AG	31287-31307	GT	AGG
(GAC)	 AG	31858-32026	GT	CGG
(TCC)	 AG	32130-32214	GT	AAG
(GTA)	 AG	32315-32428	GT	AAG
(AGG)	 AG	33042-33077	GT	CGG
(ATC)	 AG	33387-33495	GT	CAG
(ATC)	 AG	33517-33669	GT	ATG
(GCT)	 AG	33848-34084	GT	TGG
(GTG)	 AG	34344-34407	GT	AGG
(TAA)	 AG	34503-34648	GT	AGG
(GTT)	 AG	34736-34885	GT	CTG
(GTA)	 AG	35018-35233	GT	AAG
(GAT)	 AG	35424-35456	GT	AGG
-recovered snap_scaffold_39-snap.1-T1, initial, 29479, 29655
-recovered snap_scaffold_39-snap.1-T1, internal, 30208, 30300
-recovered snap_scaffold_39-snap.1-T1, internal, 30635, 30791
-recovered snap_scaffold_39-snap.1-T1, internal, 30874, 30926
-recovered snap_scaffold_39-snap.1-T1, internal, 31287, 31307
-recovered snap_scaffold_39-snap.1-T1, internal, 31858, 32026
-recovered snap_scaffold_39-snap.1-T1, internal, 32130, 32214
-recovered snap_scaffold_39-snap.1-T1, internal, 32315, 32428
-recovered snap_scaffold_39-snap.1-T1, internal, 33042, 33077
-recovered snap_scaffold_39-snap.1-T1, internal, 33387, 33495
-recovered snap_scaffold_39-snap.1-T1, internal, 33517, 33669
-recovered snap_scaffold_39-snap.1-T1, internal, 33848, 34084
-recovered snap_scaffold_39-snap.1-T1, internal, 34344, 34407
-recovered snap_scaffold_39-snap.1-T1, internal, 34503, 34648
-recovered snap_scaffold_39-snap.1-T1, internal, 34736, 34885
-recovered snap_scaffold_39-snap.1-T1, internal, 35018, 35233
-recovered snap_scaffold_39-snap.1-T1, internal, 35424, 35456
Couldn't classify 34763, 34885
Sorry, prediction GeneMark_model.106201_t fails validation.
(ATG)	 CC	29488-29655	GT	AGG
(TTT)	 AG	30208-30276	GT	TAG
(GTC)	 AG	30635-30820	GT	CAG
(GAC)	 AG	31858-32026	GT	CGG
(TCC)	 AG	32130-32214	GT	AAG
(GCG)	 AG	32852-32960	GT	TGG
(ATC)	 AG	33517-33681	GT	AGG
(GCT)	 AG	33848-34084	GT	TGG
(GTG)	 AG	34344-34407	GT	AGG
(TAA)	 AG	34503-34648	GT	AGG
(GAG)	 AG	34763-34885	GT	CTG
-recovered GeneMark_model.106201_t, initial, 29488, 29655
-recovered GeneMark_model.106201_t, internal, 30208, 30276
-recovered GeneMark_model.106201_t, internal, 30635, 30820
-recovered GeneMark_model.106201_t, internal, 31858, 32026
-recovered GeneMark_model.106201_t, internal, 32130, 32214
-recovered GeneMark_model.106201_t, internal, 32852, 32960
-recovered GeneMark_model.106201_t, internal, 33517, 33681
-recovered GeneMark_model.106201_t, internal, 33848, 34084
-recovered GeneMark_model.106201_t, internal, 34344, 34407
-recovered GeneMark_model.106201_t, internal, 34503, 34648
-recovered GeneMark_model.106201_t, internal, 34763, 34885
Valid prediction for GlimmerHMM_glimmerT_60998-T1
Valid prediction for GlimmerHMM_glimmerT_61004-T1
Valid prediction for GlimmerHMM_glimmerT_61003-T1
Couldn't classify 35754, 35820
Sorry, prediction Augustus_model.g40578.t1 fails validation.
(ATG)	 TG	28859-28893	GT	TCG
(TAT)	 AG	29472-29655	GT	AGG
(TTT)	 AG	30208-30300	GT	AGG
(GTC)	 AG	30635-30791	GT	GAG
(TCC)	 AG	30874-30926	GT	TGG
(TTT)	 AG	31287-31307	GT	AGG
(GAC)	 AG	31858-32026	GT	CGG
(TCC)	 AG	32130-32214	GT	AAG
(GTA)	 AG	32315-32441	GT	CTG
(ATC)	 AG	33517-33681	GT	AGG
(GCT)	 AG	33848-34084	GT	TGG
(GTG)	 AG	34344-34407	GT	AGG
(TAA)	 AG	34503-34648	GT	AGG
(GTT)	 AG	34736-34885	GT	CTG
(GTA)	 AG	35018-35233	GT	AAG
(GAT)	 AG	35424-35523	GT	TGG
(AAA)	 AG	35754-35820		TG
-recovered Augustus_model.g40578.t1, initial, 28859, 28893
-recovered Augustus_model.g40578.t1, internal, 29472, 29655
-recovered Augustus_model.g40578.t1, internal, 30208, 30300
-recovered Augustus_model.g40578.t1, internal, 30635, 30791
-recovered Augustus_model.g40578.t1, internal, 30874, 30926
-recovered Augustus_model.g40578.t1, internal, 31287, 31307
-recovered Augustus_model.g40578.t1, internal, 31858, 32026
-recovered Augustus_model.g40578.t1, internal, 32130, 32214
-recovered Augustus_model.g40578.t1, internal, 32315, 32441
-recovered Augustus_model.g40578.t1, internal, 33517, 33681
-recovered Augustus_model.g40578.t1, internal, 33848, 34084
-recovered Augustus_model.g40578.t1, internal, 34344, 34407
-recovered Augustus_model.g40578.t1, internal, 34503, 34648
-recovered Augustus_model.g40578.t1, internal, 34736, 34885
-recovered Augustus_model.g40578.t1, internal, 35018, 35233
-recovered Augustus_model.g40578.t1, internal, 35424, 35523
Valid prediction for Augustus_model.g40583.t1
Valid prediction for pasa_asmbl_41020.p1
Valid prediction for Augustus_model.g40579.t1
Valid prediction for GlimmerHMM_glimmerT_60999-T1
Valid prediction for snap_scaffold_39-snap.6-T1
Valid prediction for snap_scaffold_39-snap.7-T1
Couldn't classify 34586, 34648
Couldn't classify 35754, 35818
Sorry, prediction pasa_asmbl_41019.p1 fails validation.
(CCC)	 TG	34586-34648	GT	AGG
(GTT)	 AG	34736-34885	GT	CTG
(GTA)	 AG	35018-35233	GT	AAG
(GAT)	 AG	35424-35523	GT	TGG
(AAA)	 AG	35754-35818	TG	CCT
-recovered pasa_asmbl_41019.p1, internal, 34736, 34885
-recovered pasa_asmbl_41019.p1, internal, 35018, 35233
-recovered pasa_asmbl_41019.p1, internal, 35424, 35523

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

-building trellis in range 1 - 35820
-exon list size: 123


building trellis

0.8    
1.6    
2.4    
3.2    
4.0    
4.8    
5.6    
6.4    
7.2    
8.0    
8.8    
9.6    
10.4    
11.2    
12.0    
12.8    
13.6    
14.4    
15.2    
16.0    
16.8    
17.6    
18.4    
19.2    
20.0    
20.8    
21.6    
22.4    
23.2    
24.0    
24.8    
25.6    
26.4    
27.2    
28.0    
28.8    
29.6    
30.4    
31.2    
32.0    
32.8    
33.6    
34.4    
35.2    
36.0    
36.8    
37.6    
38.4    
39.2    
40.0    
40.8    
41.6    
42.4    
43.2    
44.0    
44.8    
45.6    
46.4    
47.2    
48.0    
48.8    
49.6    
50.4    
51.2    
52.0    
52.8    
53.6    
54.4    
55.2    
56.0    
56.8    
57.6    
58.4    
59.2    
60.0    
60.8    
61.6    
62.4    
63.2    
64.0    
64.8    
65.6    
66.4    
67.2    
68.0    
68.8    
69.6    
70.4    
71.2    
72.0    
72.8    
73.6    
74.4    
75.2    
76.0    
76.8    
77.6    
78.4    
79.2    
80.0    
80.8    
81.6    
82.4    
83.2    
84.0    
84.8    
85.6    
86.4    
87.2    
88.0    
88.8    
89.6    
90.4    
91.2    
92.0    
92.8    
93.6    
94.4    
95.2    
96.0    
96.8    
97.6    
98.4    
99.2    
-found 7 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 7 predictions persist after filtering for low support