-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1066

-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_62438-T1
Couldn't classify 67, 238
Couldn't classify 3230, 3337
Sorry, prediction Augustus_model.g41502.t1 fails validation.
(GGA)	 AG	67-238	GT	GCG
(GAA)	 AG	521-673	GT	GGG
(GCT)	 AG	1081-1310	GT	GGG
(GAG)	 AG	1671-1823	GT	CGG
(TGT)	 AG	3230-3337	GT	TGG
-recovered Augustus_model.g41502.t1, internal, 67, 238
-recovered Augustus_model.g41502.t1, internal, 521, 673
-recovered Augustus_model.g41502.t1, internal, 1081, 1310
-recovered Augustus_model.g41502.t1, internal, 1671, 1823
-recovered Augustus_model.g41502.t1, internal, 3230, 3337
Valid prediction for GeneMark_model.108837_t
Couldn't classify 1651, 1768
Sorry, prediction GlimmerHMM_glimmerT_62439-T1 fails validation.
(ATG)	 TG	246-293	GT	CTG
(TGT)	 AG	526-673	GT	GGG
(GCT)	 AG	1081-1306	GT	AGG
(GGC)	 AG	1651-1768	GT	CTG
-recovered GlimmerHMM_glimmerT_62439-T1, initial, 246, 293
-recovered GlimmerHMM_glimmerT_62439-T1, internal, 526, 673
-recovered GlimmerHMM_glimmerT_62439-T1, internal, 1081, 1306
-recovered GlimmerHMM_glimmerT_62439-T1, internal, 1651, 1768
Couldn't classify 67, 238
Couldn't classify 3230, 3337
Sorry, prediction snap_scaffold_1066-snap.1-T1 fails validation.
(GGA)	 AG	67-238	GT	GCG
(GAA)	 AG	521-673	GT	GGG
(GCT)	 AG	1081-1310	GT	GGG
(GAG)	 AG	1671-1823	GT	CGG
(TGT)	 AG	3230-3337	GT	TGG
-recovered snap_scaffold_1066-snap.1-T1, internal, 67, 238
-recovered snap_scaffold_1066-snap.1-T1, internal, 521, 673
-recovered snap_scaffold_1066-snap.1-T1, internal, 1081, 1310
-recovered snap_scaffold_1066-snap.1-T1, internal, 1671, 1823
-recovered snap_scaffold_1066-snap.1-T1, internal, 3230, 3337

-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 219, 521
Sorry, prediction GeneMark_model.108838_t fails validation.
(ACT)	 AG	219-521	GT	AGG
(CCG)	 AG	855-878	GT	GTG
(AGT)	 AG	1605-1644	GT	AGG
(GCG)	 AG	1670-1701	GT	AGG
(GAG)	 AG	1785-1805	GT	GTG
(AGG)	 AG	1832-1840	GT	ATG
(GGG)	 AG	1867-1875	GT	GTG
(GCT)	 AG	2184-2357	GT	GAG
(AGG)	 AG	2379-2399	GT	GAG
(GAG)	 AG	2424-2450	GT	CGG
(GGA)	 AG	2478-2588	GT	AGG
(TCT)	 AG	2723-2821	GT	GGG
(AGA)	 AG	2909-3004	GT	GAG
(GGG)	 AG	3045-3050	GT	GAG
(AGT)	 AG	3075-3090	TA	AGT
-recovered GeneMark_model.108838_t, terminal, 3075, 3090
-recovered GeneMark_model.108838_t, internal, 219, 521
-recovered GeneMark_model.108838_t, internal, 855, 878
-recovered GeneMark_model.108838_t, internal, 1605, 1644
-recovered GeneMark_model.108838_t, internal, 1670, 1701
-recovered GeneMark_model.108838_t, internal, 1785, 1805
-recovered GeneMark_model.108838_t, internal, 1832, 1840
-recovered GeneMark_model.108838_t, internal, 1867, 1875
-recovered GeneMark_model.108838_t, internal, 2184, 2357
-recovered GeneMark_model.108838_t, internal, 2379, 2399
-recovered GeneMark_model.108838_t, internal, 2424, 2450
-recovered GeneMark_model.108838_t, internal, 2478, 2588
-recovered GeneMark_model.108838_t, internal, 2723, 2821
-recovered GeneMark_model.108838_t, internal, 2909, 3004
-recovered GeneMark_model.108838_t, internal, 3045, 3050

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

-building trellis in range 1 - 3401
-exon list size: 44


building trellis

2.2    
4.3    
6.5    
8.7    
10.9    
13.0    
15.2    
17.4    
19.6    
21.7    
23.9    
26.1    
28.3    
30.4    
32.6    
34.8    
37.0    
39.1    
41.3    
43.5    
45.7    
47.8    
50.0    
52.2    
54.3    
56.5    
58.7    
60.9    
63.0    
65.2    
67.4    
69.6    
71.7    
73.9    
76.1    
78.3    
80.4    
82.6    
84.8    
87.0    
89.1    
91.3    
93.5    
95.7    
97.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support