-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_109

-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_61304-T1
Valid prediction for snap_scaffold_109-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_61303-T1
Valid prediction for GeneMark_model.106594_t
Valid prediction for Augustus_model.g40779.t1
Valid prediction for snap_scaffold_109-snap.2-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 432, 759
Sorry, prediction snap_scaffold_109-snap.4-T1 fails validation.
(CTG)	 AG	432-759	GT	GAG
(ATC)	 AG	882-1031	GT	TGG
(CCC)	 AG	1172-1355	GT	CGG
(GCC)	 AG	1460-1608	GT	GAG
(TCT)	 AG	1714-1959	GT	AAG
(GTG)	 AG	2032-2191	GT	CTG
(TTG)	 AG	2638-2745	AA	AAA
add_exon() Sorry, snap_scaffold_109-snap.4-T1 432-759-terminal-3 is invalid.
-recovered snap_scaffold_109-snap.4-T1, terminal, 432, 759
-recovered snap_scaffold_109-snap.4-T1, terminal, 2638, 2745
-recovered snap_scaffold_109-snap.4-T1, internal, 432, 759
-recovered snap_scaffold_109-snap.4-T1, internal, 882, 1031
-recovered snap_scaffold_109-snap.4-T1, internal, 1172, 1355
-recovered snap_scaffold_109-snap.4-T1, internal, 1460, 1608
-recovered snap_scaffold_109-snap.4-T1, internal, 1714, 1959
-recovered snap_scaffold_109-snap.4-T1, internal, 2032, 2191
Couldn't classify 209, 225
Sorry, prediction GeneMark_model.106595_t fails validation.
(AAC)	 AG	209-225	GT	CCG
(AGT)	 AG	490-759	GT	GAG
(ATC)	 AG	882-1031	GT	TGG
(CTA)	 AG	1196-1355	GT	CGG
(GCC)	 AG	1460-1608	GT	GAG
(GAC)	 AG	1753-2191	GT	CTG
(GTG)	 AG	2475-2488	GT	AGG
(TGA)	 AG	2655-2745	AA	AAA
add_exon() Sorry, GeneMark_model.106595_t 490-759-terminal-1 is invalid.
-recovered GeneMark_model.106595_t, terminal, 490, 759
-recovered GeneMark_model.106595_t, terminal, 2655, 2745
-recovered GeneMark_model.106595_t, internal, 209, 225
-recovered GeneMark_model.106595_t, internal, 490, 759
-recovered GeneMark_model.106595_t, internal, 882, 1031
-recovered GeneMark_model.106595_t, internal, 1196, 1355
-recovered GeneMark_model.106595_t, internal, 1460, 1608
-recovered GeneMark_model.106595_t, internal, 1753, 2191
-recovered GeneMark_model.106595_t, internal, 2475, 2488
Couldn't classify 432, 755
Sorry, prediction GlimmerHMM_glimmerT_61305-T1 fails validation.
(CTG)	 AG	432-755	GT	CGG
(ATC)	 AG	882-1031	GT	TGG
(TAA)	 AG	1168-1355	GT	CGG
(GCC)	 AG	1460-1608	GT	GAG
(TCT)	 AG	1714-1959	GT	AAG
(GTG)	 AG	2032-2191	GT	CTG
(GTG)	 AG	2475-2573	TG	GAT
-recovered GlimmerHMM_glimmerT_61305-T1, terminal, 2475, 2573
-recovered GlimmerHMM_glimmerT_61305-T1, internal, 432, 755
-recovered GlimmerHMM_glimmerT_61305-T1, internal, 882, 1031
-recovered GlimmerHMM_glimmerT_61305-T1, internal, 1168, 1355
-recovered GlimmerHMM_glimmerT_61305-T1, internal, 1460, 1608
-recovered GlimmerHMM_glimmerT_61305-T1, internal, 1714, 1959
-recovered GlimmerHMM_glimmerT_61305-T1, internal, 2032, 2191
Valid prediction for snap_scaffold_109-snap.1-T1
Couldn't classify 490, 755
Sorry, prediction Augustus_model.g40780.t1 fails validation.
(AGT)	 AG	490-755	GT	CGG
(CAG)	 AG	1231-1355	GT	CGG
(GCC)	 AG	1460-1608	GT	GAG
(TCT)	 AG	1714-1959	GT	AAG
(GTG)	 AG	2032-2191	GT	CTG
(GTG)	 AG	2475-2550	GT	CTG
(TTG)	 AG	2638-2645	AG	AGA
-recovered Augustus_model.g40780.t1, terminal, 2638, 2645
-recovered Augustus_model.g40780.t1, internal, 490, 755
-recovered Augustus_model.g40780.t1, internal, 1231, 1355
-recovered Augustus_model.g40780.t1, internal, 1460, 1608
-recovered Augustus_model.g40780.t1, internal, 1714, 1959
-recovered Augustus_model.g40780.t1, internal, 2032, 2191
-recovered Augustus_model.g40780.t1, internal, 2475, 2550

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

-building trellis in range 1 - 15019
-exon list size: 62


building trellis

1.6    
3.1    
4.7    
6.2    
7.8    
9.4    
10.9    
12.5    
14.1    
15.6    
17.2    
18.8    
20.3    
21.9    
23.4    
25.0    
26.6    
28.1    
29.7    
31.2    
32.8    
34.4    
35.9    
37.5    
39.1    
40.6    
42.2    
43.8    
45.3    
46.9    
48.4    
50.0    
51.6    
53.1    
54.7    
56.2    
57.8    
59.4    
60.9    
62.5    
64.1    
65.6    
67.2    
68.8    
70.3    
71.9    
73.4    
75.0    
76.6    
78.1    
79.7    
81.2    
82.8    
84.4    
85.9    
87.5    
89.1    
90.6    
92.2    
93.8    
95.3    
96.9    
98.4    
-found 3 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support