-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_40

-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 Augustus_model.g40589.t1
Valid prediction for GeneMark_model.106215_t
Valid prediction for GlimmerHMM_glimmerT_61008-T1
Valid prediction for snap_scaffold_40-snap.7-T1
Valid prediction for snap_scaffold_40-snap.5-T1
Valid prediction for GlimmerHMM_glimmerT_61012-T1
Valid prediction for GeneMark_model.106212_t
Valid prediction for GlimmerHMM_glimmerT_61010-T1
Valid prediction for snap_scaffold_40-snap.3-T1
Valid prediction for GeneMark_model.106214_t
Valid prediction for Augustus_model.g40586.t1
Valid prediction for GlimmerHMM_glimmerT_61011-T1
Valid prediction for GlimmerHMM_glimmerT_61013-T1
Couldn't classify 31101, 31272
Sorry, prediction GlimmerHMM_glimmerT_61015-T1 fails validation.
(ATG)	 CC	30483-30709	GT	TGG
(GCG)	 AG	31101-31272	GT	AGG
-recovered GlimmerHMM_glimmerT_61015-T1, initial, 30483, 30709
-recovered GlimmerHMM_glimmerT_61015-T1, internal, 31101, 31272
Valid prediction for Augustus_model.g40588.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: -)Couldn't classify 1327, 1532
Sorry, prediction GeneMark_model.106216_t fails validation.
(GAA)	 AG	1327-1532	GT	CGG
(GTT)	 AG	1577-1663	GT	CCG
(CTG)	 AG	1803-1915	GT	CGG
(AAG)	 AG	1986-2251	GT	GGG
(AAG)	 AG	2367-2398	CT	AGC
-recovered GeneMark_model.106216_t, terminal, 2367, 2398
-recovered GeneMark_model.106216_t, internal, 1327, 1532
-recovered GeneMark_model.106216_t, internal, 1577, 1663
-recovered GeneMark_model.106216_t, internal, 1803, 1915
-recovered GeneMark_model.106216_t, internal, 1986, 2251
Valid prediction for GlimmerHMM_glimmerT_61006-T1
Valid prediction for GlimmerHMM_glimmerT_61009-T1
Valid prediction for GeneMark_model.106211_t
Valid prediction for GlimmerHMM_glimmerT_61005-T1
Valid prediction for GlimmerHMM_glimmerT_61007-T1
Valid prediction for Augustus_model.g40584.t1
Couldn't classify 31310, 31760
Sorry, prediction GeneMark_model.106210_t fails validation.
(ATG)	 AA	29491-29561	GT	AAG
(ATA)	 AG	29643-29790	GT	TGG
(AGG)	 AG	30032-30070	GT	TGG
(AAG)	 AG	30745-30783	GT	TGG
(CAC)	 AG	30881-30962	GT	TGG
(ATG)	 AG	31310-31760	GT	AGG
-recovered GeneMark_model.106210_t, initial, 29491, 29561
add_exon() Sorry, GeneMark_model.106210_t 31310-31760-initial-1 is invalid.
-recovered GeneMark_model.106210_t, initial, 31310, 31760
-recovered GeneMark_model.106210_t, internal, 29643, 29790
-recovered GeneMark_model.106210_t, internal, 30032, 30070
-recovered GeneMark_model.106210_t, internal, 30745, 30783
-recovered GeneMark_model.106210_t, internal, 30881, 30962
-recovered GeneMark_model.106210_t, internal, 31310, 31760
Valid prediction for GlimmerHMM_glimmerT_61014-T1
Valid prediction for snap_scaffold_40-snap.4-T1
Couldn't classify 4735, 5271
Sorry, prediction pasa_asmbl_43644.p1 fails validation.
(CCC)	 AA	4735-5271	AC	TGA
Valid prediction for snap_scaffold_40-snap.1-T1
Valid prediction for Augustus_model.g40587.t1
Valid prediction for snap_scaffold_40-snap.2-T1
Valid prediction for Augustus_model.g40585.t1
Valid prediction for GeneMark_model.106213_t
Valid prediction for snap_scaffold_40-snap.6-T1

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

-building trellis in range 1 - 32659
-exon list size: 111


building trellis

0.9    
1.8    
2.7    
3.5    
4.4    
5.3    
6.2    
7.1    
8.0    
8.8    
9.7    
10.6    
11.5    
12.4    
13.3    
14.2    
15.0    
15.9    
16.8    
17.7    
18.6    
19.5    
20.4    
21.2    
22.1    
23.0    
23.9    
24.8    
25.7    
26.5    
27.4    
28.3    
29.2    
30.1    
31.0    
31.9    
32.7    
33.6    
34.5    
35.4    
36.3    
37.2    
38.1    
38.9    
39.8    
40.7    
41.6    
42.5    
43.4    
44.2    
45.1    
46.0    
46.9    
47.8    
48.7    
49.6    
50.4    
51.3    
52.2    
53.1    
54.0    
54.9    
55.8    
56.6    
57.5    
58.4    
59.3    
60.2    
61.1    
61.9    
62.8    
63.7    
64.6    
65.5    
66.4    
67.3    
68.1    
69.0    
69.9    
70.8    
71.7    
72.6    
73.5    
74.3    
75.2    
76.1    
77.0    
77.9    
78.8    
79.6    
80.5    
81.4    
82.3    
83.2    
84.1    
85.0    
85.8    
86.7    
87.6    
88.5    
89.4    
90.3    
91.2    
92.0    
92.9    
93.8    
94.7    
95.6    
96.5    
97.3    
98.2    
99.1    
-found 7 predictions from path traversal

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