-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_723

-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: +)
-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 376, 503
Sorry, prediction GlimmerHMM_glimmerT_62163-T1 fails validation.
(GTA)	 AG	376-503	GT	TGG
(AAG)	 AG	831-1029	GT	GGG
(GTT)	 AG	1140-1189	GT	AGG
(GAC)	 AG	1484-1561	GT	GGG
(GTC)	 AG	2086-2142	GT	GGG
(CTA)	 AG	2979-3113	GT	AGG
(GTG)	 AG	3720-3908	GT	AGG
(GAC)	 AG	4016-4140	GT	AGG
(AAC)	 AG	4458-4473	CC	GAC
-recovered GlimmerHMM_glimmerT_62163-T1, terminal, 4458, 4473
-recovered GlimmerHMM_glimmerT_62163-T1, internal, 376, 503
-recovered GlimmerHMM_glimmerT_62163-T1, internal, 831, 1029
-recovered GlimmerHMM_glimmerT_62163-T1, internal, 1140, 1189
-recovered GlimmerHMM_glimmerT_62163-T1, internal, 1484, 1561
-recovered GlimmerHMM_glimmerT_62163-T1, internal, 2086, 2142
-recovered GlimmerHMM_glimmerT_62163-T1, internal, 2979, 3113
-recovered GlimmerHMM_glimmerT_62163-T1, internal, 3720, 3908
-recovered GlimmerHMM_glimmerT_62163-T1, internal, 4016, 4140
Couldn't classify 376, 503
Couldn't classify 4566, 4744
Sorry, prediction Augustus_model.g41319.t1 fails validation.
(GTA)	 AG	376-503	GT	TGG
(AAG)	 AG	831-1029	GT	GGG
(GTT)	 AG	1140-1189	GT	AGG
(GAC)	 AG	1484-1561	GT	GGG
(GTC)	 AG	2086-2142	GT	GGG
(AGA)	 AG	2299-2370	GT	CGG
(CTA)	 AG	2979-3113	GT	AGG
(GTG)	 AG	3720-3908	GT	AGG
(GAC)	 AG	4016-4140	GT	AGG
(GAG)	 AG	4566-4744	GT	TGG
-recovered Augustus_model.g41319.t1, internal, 376, 503
-recovered Augustus_model.g41319.t1, internal, 831, 1029
-recovered Augustus_model.g41319.t1, internal, 1140, 1189
-recovered Augustus_model.g41319.t1, internal, 1484, 1561
-recovered Augustus_model.g41319.t1, internal, 2086, 2142
-recovered Augustus_model.g41319.t1, internal, 2299, 2370
-recovered Augustus_model.g41319.t1, internal, 2979, 3113
-recovered Augustus_model.g41319.t1, internal, 3720, 3908
-recovered Augustus_model.g41319.t1, internal, 4016, 4140
-recovered Augustus_model.g41319.t1, internal, 4566, 4744
Couldn't classify 4566, 4744
Sorry, prediction snap_scaffold_723-snap.1-T1 fails validation.
(ATG)	 CC	2080-2142	GT	GGG
(CTA)	 AG	2979-3113	GT	AGG
(GTG)	 AG	3720-3908	GT	AGG
(GAC)	 AG	4016-4140	GT	AGG
(GAG)	 AG	4566-4744	GT	TGG
-recovered snap_scaffold_723-snap.1-T1, initial, 2080, 2142
-recovered snap_scaffold_723-snap.1-T1, internal, 2979, 3113
-recovered snap_scaffold_723-snap.1-T1, internal, 3720, 3908
-recovered snap_scaffold_723-snap.1-T1, internal, 4016, 4140
-recovered snap_scaffold_723-snap.1-T1, internal, 4566, 4744
Couldn't classify 10, 60
Sorry, prediction GeneMark_model.108260_t fails validation.
(ACC)	 AG	10-60	GT	GGG
(GTA)	 AG	376-503	GT	TGG
(AAG)	 AG	831-1029	GT	GGG
(GTT)	 AG	1140-1189	GT	AGG
(GAC)	 AG	1484-1567	AC	AGA
-recovered GeneMark_model.108260_t, terminal, 1484, 1567
-recovered GeneMark_model.108260_t, internal, 10, 60
-recovered GeneMark_model.108260_t, internal, 376, 503
-recovered GeneMark_model.108260_t, internal, 831, 1029
-recovered GeneMark_model.108260_t, internal, 1140, 1189
Valid prediction for GeneMark_model.108259_t
Couldn't classify 4566, 4746
Sorry, prediction pasa_asmbl_51573.p1 fails validation.
(ATG)	 GA	2302-2370	GT	CGG
(CTA)	 AG	2979-3113	GT	AGG
(GTG)	 AG	3720-3908	GT	AGG
(GAC)	 AG	4016-4140	GT	AGG
(GAG)	 AG	4566-4746	GA	GTG
-recovered pasa_asmbl_51573.p1, initial, 2302, 2370
-recovered pasa_asmbl_51573.p1, internal, 2979, 3113
-recovered pasa_asmbl_51573.p1, internal, 3720, 3908
-recovered pasa_asmbl_51573.p1, internal, 4016, 4140
Couldn't classify 4566, 4784
Sorry, prediction GeneMark_model.108258_t fails validation.
(ATG)	 CG	3732-3908	GT	AGG
(GAC)	 AG	4016-4140	GT	AGG
(GAG)	 AG	4566-4784	GT	GAG
-recovered GeneMark_model.108258_t, initial, 3732, 3908
-recovered GeneMark_model.108258_t, internal, 4016, 4140
-recovered GeneMark_model.108258_t, internal, 4566, 4784
Couldn't classify 376, 503
Sorry, prediction snap_scaffold_723-snap.2-T1 fails validation.
(GTA)	 AG	376-503	GT	TGG
(AAG)	 AG	831-1029	GT	GGG
(GTT)	 AG	1140-1189	GT	AGG
(GAC)	 AG	1484-1567	AC	AGA
-recovered snap_scaffold_723-snap.2-T1, terminal, 1484, 1567
-recovered snap_scaffold_723-snap.2-T1, internal, 376, 503
-recovered snap_scaffold_723-snap.2-T1, internal, 831, 1029
-recovered snap_scaffold_723-snap.2-T1, internal, 1140, 1189

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

-building trellis in range 1 - 4808
-exon list size: 34


building trellis

2.8    
5.6    
8.3    
11.1    
13.9    
16.7    
19.4    
22.2    
25.0    
27.8    
30.6    
33.3    
36.1    
38.9    
41.7    
44.4    
47.2    
50.0    
52.8    
55.6    
58.3    
61.1    
63.9    
66.7    
69.4    
72.2    
75.0    
77.8    
80.6    
83.3    
86.1    
88.9    
91.7    
94.4    
97.2    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support