-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/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_60973-T1
Valid prediction for snap_scaffold_35-snap.10-T1
Valid prediction for snap_scaffold_35-snap.8-T1
Valid prediction for GlimmerHMM_glimmerT_60976-T1
Valid prediction for snap_scaffold_35-snap.7-T1
Couldn't classify 398, 547
Sorry, prediction GeneMark_model.106168_t fails validation.
(ATT)	 AG	398-547	GT	AGG
(AGA)	 AG	743-853	GT	CGG
(AGA)	 AG	1345-1485	GT	AGG
(GTG)	 AG	1620-1733	GT	CTG
(ACT)	 AG	1989-2014	GT	GAG
(GAA)	 AG	2044-2131	CA	AAC
-recovered GeneMark_model.106168_t, terminal, 2044, 2131
-recovered GeneMark_model.106168_t, internal, 398, 547
-recovered GeneMark_model.106168_t, internal, 743, 853
-recovered GeneMark_model.106168_t, internal, 1345, 1485
-recovered GeneMark_model.106168_t, internal, 1620, 1733
-recovered GeneMark_model.106168_t, internal, 1989, 2014
Valid prediction for Augustus_model.g40563.t1
Valid prediction for Augustus_model.g40561.t1
Valid prediction for snap_scaffold_35-snap.9-T1
Valid prediction for Augustus_model.g40564.t1
Valid prediction for GlimmerHMM_glimmerT_60979-T1
Valid prediction for snap_scaffold_35-snap.5-T1
Valid prediction for snap_scaffold_35-snap.2-T1
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
Valid prediction for GeneMark_model.106173_t
Couldn't classify 113, 225
Sorry, prediction Augustus_model.g40559.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.g40559.t1, terminal, 3902, 4041
-recovered Augustus_model.g40559.t1, internal, 113, 225
-recovered Augustus_model.g40559.t1, internal, 398, 547
-recovered Augustus_model.g40559.t1, internal, 743, 853
-recovered Augustus_model.g40559.t1, internal, 1345, 1485
-recovered Augustus_model.g40559.t1, internal, 1620, 1733
-recovered Augustus_model.g40559.t1, internal, 1835, 1907
-recovered Augustus_model.g40559.t1, internal, 1989, 2127
-recovered Augustus_model.g40559.t1, internal, 2224, 2273
Valid prediction for GlimmerHMM_glimmerT_60978-T1
Valid prediction for GlimmerHMM_glimmerT_60977-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_60982-T1
Valid prediction for Augustus_model.g40560.t1
Valid prediction for GlimmerHMM_glimmerT_60975-T1
Valid prediction for snap_scaffold_35-snap.12-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_35-snap.13-T1
Valid prediction for GeneMark_model.106171_t
Valid prediction for GeneMark_model.106169_t
Couldn't classify 32032, 32337
Sorry, prediction pasa_asmbl_40981.p1 fails validation.
(GGA)	 CA	32032-32337	AC	AAA
Valid prediction for Augustus_model.g40566.t1
Valid prediction for GlimmerHMM_glimmerT_60980-T1
Valid prediction for GlimmerHMM_glimmerT_60981-T1
Valid prediction for GeneMark_model.106175_t
Valid prediction for snap_scaffold_35-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_60974-T1
Valid prediction for Augustus_model.g40567.t1
Valid prediction for snap_scaffold_35-snap.6-T1
Valid prediction for snap_scaffold_35-snap.4-T1
Valid prediction for snap_scaffold_35-snap.3-T1
Valid prediction for snap_scaffold_35-snap.14-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_35-snap.15-T1
Valid prediction for GeneMark_model.106170_t
Valid prediction for Augustus_model.g40562.t1
Couldn't classify 7949, 8305
Sorry, prediction pasa_asmbl_40982.p1 fails validation.
(AAA)	 GC	7949-8305	GA	GAG
Valid prediction for Augustus_model.g40565.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: 116


building trellis

0.8    
1.7    
2.5    
3.4    
4.2    
5.1    
5.9    
6.8    
7.6    
8.5    
9.3    
10.2    
11.0    
11.9    
12.7    
13.6    
14.4    
15.3    
16.1    
16.9    
17.8    
18.6    
19.5    
20.3    
21.2    
22.0    
22.9    
23.7    
24.6    
25.4    
26.3    
27.1    
28.0    
28.8    
29.7    
30.5    
31.4    
32.2    
33.1    
33.9    
34.7    
35.6    
36.4    
37.3    
38.1    
39.0    
39.8    
40.7    
41.5    
42.4    
43.2    
44.1    
44.9    
45.8    
46.6    
47.5    
48.3    
49.2    
50.0    
50.8    
51.7    
52.5    
53.4    
54.2    
55.1    
55.9    
56.8    
57.6    
58.5    
59.3    
60.2    
61.0    
61.9    
62.7    
63.6    
64.4    
65.3    
66.1    
66.9    
67.8    
68.6    
69.5    
70.3    
71.2    
72.0    
72.9    
73.7    
74.6    
75.4    
76.3    
77.1    
78.0    
78.8    
79.7    
80.5    
81.4    
82.2    
83.1    
83.9    
84.7    
85.6    
86.4    
87.3    
88.1    
89.0    
89.8    
90.7    
91.5    
92.4    
93.2    
94.1    
94.9    
95.8    
96.6    
97.5    
98.3    
99.2    
-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