-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_54

-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_54-snap.7-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.106291_t
Couldn't classify 27209, 27233
Sorry, prediction GeneMark_model.106289_t fails validation.
(ATG)	 GG	17438-17454	GT	GGG
(GGT)	 AG	17488-17505	GT	GGG
(GGA)	 AG	17556-17573	GT	GGG
(GGT)	 AG	17625-17642	GT	GGG
(GGT)	 AG	17676-17785	GT	GAG
(TGA)	 AG	20027-20098	GT	TGG
(ACG)	 AG	21497-21537	GT	CGG
(CCT)	 AG	23578-23718	GT	CGG
(GAC)	 AG	23973-24194	GT	TGG
(GTG)	 AG	24489-24576	GT	AGG
(AGG)	 AG	24663-24792	GT	CCG
(AGG)	 AG	26433-26442	GT	AGG
(AGG)	 AG	26468-26477	GT	AGG
(AGG)	 AG	26503-26512	GT	AGG
(AGG)	 AG	26538-26547	GT	AGG
(AGG)	 AG	26573-26582	GT	AGG
(AGG)	 AG	26608-26617	GT	AGG
(AGA)	 AG	26730-26867	GT	AGG
(GGA)	 AG	26908-26919	GT	GAG
(GAG)	 AG	27209-27233	GT	CAG
-recovered GeneMark_model.106289_t, initial, 17438, 17454
-recovered GeneMark_model.106289_t, internal, 17488, 17505
-recovered GeneMark_model.106289_t, internal, 17556, 17573
-recovered GeneMark_model.106289_t, internal, 17625, 17642
-recovered GeneMark_model.106289_t, internal, 17676, 17785
-recovered GeneMark_model.106289_t, internal, 20027, 20098
-recovered GeneMark_model.106289_t, internal, 21497, 21537
-recovered GeneMark_model.106289_t, internal, 23578, 23718
-recovered GeneMark_model.106289_t, internal, 23973, 24194
-recovered GeneMark_model.106289_t, internal, 24489, 24576
-recovered GeneMark_model.106289_t, internal, 24663, 24792
-recovered GeneMark_model.106289_t, internal, 26433, 26442
-recovered GeneMark_model.106289_t, internal, 26468, 26477
-recovered GeneMark_model.106289_t, internal, 26503, 26512
-recovered GeneMark_model.106289_t, internal, 26538, 26547
-recovered GeneMark_model.106289_t, internal, 26573, 26582
-recovered GeneMark_model.106289_t, internal, 26608, 26617
-recovered GeneMark_model.106289_t, internal, 26730, 26867
-recovered GeneMark_model.106289_t, internal, 26908, 26919
-recovered GeneMark_model.106289_t, internal, 27209, 27233
Couldn't classify 20027, 20280
Sorry, prediction pasa_asmbl_46504.p1 fails validation.
(ATG)	 TA	19758-19812	GT	CTG
(TGA)	 AG	20027-20280	GA	GGG
-recovered pasa_asmbl_46504.p1, initial, 19758, 19812
Valid prediction for snap_scaffold_54-snap.5-T1
Valid prediction for Augustus_model.g40633.t1
Valid prediction for snap_scaffold_54-snap.4-T1
Valid prediction for snap_scaffold_54-snap.6-T1
Valid prediction for GeneMark_model.106290_t
Valid prediction for GlimmerHMM_glimmerT_61080-T1
Valid prediction for GlimmerHMM_glimmerT_61077-T1
Couldn't classify 74, 110
Sorry, prediction snap_scaffold_54-snap.9-T1 fails validation.
(TCA)	 AG	74-110	GT	AGG
(AAC)	 AG	191-1157	GT	AGG
(GCC)	 AG	1365-1735	GG	GAG
-recovered snap_scaffold_54-snap.9-T1, terminal, 1365, 1735
-recovered snap_scaffold_54-snap.9-T1, internal, 74, 110
-recovered snap_scaffold_54-snap.9-T1, internal, 191, 1157
Valid prediction for snap_scaffold_54-snap.2-T1
Couldn't classify 191, 1157
Sorry, prediction Augustus_model.g40634.t1 fails validation.
(AAC)	 AG	191-1157	GT	AGG
(GCC)	 AG	1365-1722	GT	CAG
(CTC)	 AG	1979-2087	GT	TGG
(AAG)	 AG	2216-2321	GT	AAG
(GTC)	 AG	2510-2652	AG	AGA
-recovered Augustus_model.g40634.t1, terminal, 2510, 2652
-recovered Augustus_model.g40634.t1, internal, 191, 1157
-recovered Augustus_model.g40634.t1, internal, 1365, 1722
-recovered Augustus_model.g40634.t1, internal, 1979, 2087
-recovered Augustus_model.g40634.t1, internal, 2216, 2321
Couldn't classify 191, 1157
Sorry, prediction GeneMark_model.106292_t fails validation.
(AAC)	 AG	191-1157	GT	AGG
(GCC)	 AG	1365-1722	GT	CAG
(GGT)	 AG	1797-1835	GT	GAG
(CGC)	 AG	1958-2067	GT	CCG
(GTC)	 AG	2510-2652	AG	AGA
-recovered GeneMark_model.106292_t, terminal, 2510, 2652
-recovered GeneMark_model.106292_t, internal, 191, 1157
-recovered GeneMark_model.106292_t, internal, 1365, 1722
-recovered GeneMark_model.106292_t, internal, 1797, 1835
-recovered GeneMark_model.106292_t, internal, 1958, 2067
Valid prediction for snap_scaffold_54-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_61078-T1
Valid prediction for GlimmerHMM_glimmerT_61079-T1
Couldn't classify 191, 1157
Sorry, prediction GlimmerHMM_glimmerT_61081-T1 fails validation.
(AAC)	 AG	191-1157	GT	AGG
(GCC)	 AG	1365-1735	GG	GAG
-recovered GlimmerHMM_glimmerT_61081-T1, terminal, 1365, 1735
-recovered GlimmerHMM_glimmerT_61081-T1, internal, 191, 1157
Valid prediction for Augustus_model.g40631.t1
Valid prediction for snap_scaffold_54-snap.8-T1
Valid prediction for HiQ_model.g40632.t1
Couldn't classify 26933, 26997
Sorry, prediction snap_scaffold_54-snap.1-T1 fails validation.
(ATG)	 GG	26383-26617	GT	AGG
(GAG)	 AG	26933-26997	GT	CGG
-recovered snap_scaffold_54-snap.1-T1, initial, 26383, 26617
-recovered snap_scaffold_54-snap.1-T1, internal, 26933, 26997

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

-building trellis in range 1 - 27500
-exon list size: 114


building trellis

0.9    
1.7    
2.6    
3.4    
4.3    
5.2    
6.0    
6.9    
7.8    
8.6    
9.5    
10.3    
11.2    
12.1    
12.9    
13.8    
14.7    
15.5    
16.4    
17.2    
18.1    
19.0    
19.8    
20.7    
21.6    
22.4    
23.3    
24.1    
25.0    
25.9    
26.7    
27.6    
28.4    
29.3    
30.2    
31.0    
31.9    
32.8    
33.6    
34.5    
35.3    
36.2    
37.1    
37.9    
38.8    
39.7    
40.5    
41.4    
42.2    
43.1    
44.0    
44.8    
45.7    
46.6    
47.4    
48.3    
49.1    
50.0    
50.9    
51.7    
52.6    
53.4    
54.3    
55.2    
56.0    
56.9    
57.8    
58.6    
59.5    
60.3    
61.2    
62.1    
62.9    
63.8    
64.7    
65.5    
66.4    
67.2    
68.1    
69.0    
69.8    
70.7    
71.6    
72.4    
73.3    
74.1    
75.0    
75.9    
76.7    
77.6    
78.4    
79.3    
80.2    
81.0    
81.9    
82.8    
83.6    
84.5    
85.3    
86.2    
87.1    
87.9    
88.8    
89.7    
90.5    
91.4    
92.2    
93.1    
94.0    
94.8    
95.7    
96.6    
97.4    
98.3    
99.1    
-found 6 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 6 predictions persist after filtering for low support