-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1133

-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: +)Couldn't classify 635, 841
Sorry, prediction Augustus_model.g41545.t1 fails validation.
(CTG)	 AG	635-841	GT	CGG
(TCT)	 AG	1347-1490	GT	AGG
(CAA)	 AG	1736-1924	GT	AGG
(CAC)	 AG	2230-2347	GT	GGG
(AGA)	 AG	2598-2653	GT	AGG
(GAA)	 AG	2848-2961	GA	AAG
-recovered Augustus_model.g41545.t1, terminal, 2848, 2961
-recovered Augustus_model.g41545.t1, internal, 635, 841
-recovered Augustus_model.g41545.t1, internal, 1347, 1490
-recovered Augustus_model.g41545.t1, internal, 1736, 1924
-recovered Augustus_model.g41545.t1, internal, 2230, 2347
-recovered Augustus_model.g41545.t1, internal, 2598, 2653
Couldn't classify 635, 841
Couldn't classify 2848, 2957
Sorry, prediction snap_scaffold_1133-snap.1-T1 fails validation.
(CTG)	 AG	635-841	GT	CGG
(TCT)	 AG	1347-1529	GT	TGG
(CAA)	 AG	1736-1924	GT	AGG
(CAC)	 AG	2230-2347	GT	GGG
(AGA)	 AG	2598-2653	GT	AGG
(GAA)	 AG	2848-2957	GT	GAG
-recovered snap_scaffold_1133-snap.1-T1, internal, 635, 841
-recovered snap_scaffold_1133-snap.1-T1, internal, 1347, 1529
-recovered snap_scaffold_1133-snap.1-T1, internal, 1736, 1924
-recovered snap_scaffold_1133-snap.1-T1, internal, 2230, 2347
-recovered snap_scaffold_1133-snap.1-T1, internal, 2598, 2653
-recovered snap_scaffold_1133-snap.1-T1, internal, 2848, 2957
Valid prediction for GlimmerHMM_glimmerT_62490-T1
Couldn't classify 13, 84
Sorry, prediction GeneMark_model.108943_t fails validation.
(GAA)	 AG	13-84	GT	GGG
(ACC)	 AG	105-131	GT	GGG
(GGA)	 AG	155-254	GT	ATG
(CTG)	 AG	635-841	GT	CGG
(TCT)	 AG	1347-1529	GT	TGG
(CAA)	 AG	1736-1948	TG	GAT
-recovered GeneMark_model.108943_t, terminal, 1736, 1948
-recovered GeneMark_model.108943_t, internal, 13, 84
-recovered GeneMark_model.108943_t, internal, 105, 131
-recovered GeneMark_model.108943_t, internal, 155, 254
-recovered GeneMark_model.108943_t, internal, 635, 841
-recovered GeneMark_model.108943_t, internal, 1347, 1529
Couldn't classify 2848, 2957
Sorry, prediction GlimmerHMM_glimmerT_62491-T1 fails validation.
(ATG)	 GC	1322-1324	GT	TGG
(TCT)	 AG	1347-1490	GT	AGG
(CAA)	 AG	1736-1924	GT	AGG
(CAC)	 AG	2230-2347	GT	GGG
(AGA)	 AG	2598-2653	GT	AGG
(GAA)	 AG	2848-2957	GT	GAG
-recovered GlimmerHMM_glimmerT_62491-T1, initial, 1322, 1324
-recovered GlimmerHMM_glimmerT_62491-T1, internal, 1347, 1490
-recovered GlimmerHMM_glimmerT_62491-T1, internal, 1736, 1924
-recovered GlimmerHMM_glimmerT_62491-T1, internal, 2230, 2347
-recovered GlimmerHMM_glimmerT_62491-T1, internal, 2598, 2653
-recovered GlimmerHMM_glimmerT_62491-T1, internal, 2848, 2957
Couldn't classify 635, 841
Couldn't classify 2848, 2955
Sorry, prediction pasa_asmbl_7376.p1 fails validation.
(CTG)	 AG	635-841	GT	CGG
(TCT)	 AG	1347-1490	GT	AGG
(CAA)	 AG	1736-1924	GT	AGG
(CAC)	 AG	2230-2347	GT	GGG
(AGA)	 AG	2598-2653	GT	AGG
(GAA)	 AG	2848-2955	GA	AGG
-recovered pasa_asmbl_7376.p1, internal, 635, 841
-recovered pasa_asmbl_7376.p1, internal, 1347, 1490
-recovered pasa_asmbl_7376.p1, internal, 1736, 1924
-recovered pasa_asmbl_7376.p1, internal, 2230, 2347
-recovered pasa_asmbl_7376.p1, internal, 2598, 2653

-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 268, 353
Sorry, prediction GeneMark_model.108944_t fails validation.
(TTC)	 AG	268-353	GT	AGG
(AGA)	 AG	687-773	GT	CCG
(CAA)	 AG	799-960	GT	TGG
(GAA)	 AG	1000-1147	AC	GAA
-recovered GeneMark_model.108944_t, terminal, 1000, 1147
-recovered GeneMark_model.108944_t, internal, 268, 353
-recovered GeneMark_model.108944_t, internal, 687, 773
-recovered GeneMark_model.108944_t, internal, 799, 960

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

-building trellis in range 1 - 3186
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-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