-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1147

-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 46, 214
Couldn't classify 429, 619
Sorry, prediction pasa_asmbl_7384.p1 fails validation.
(TTT)	 AG	46-214	GT	CAG
(ATG)	 AG	429-619	AC	GCA
-recovered pasa_asmbl_7384.p1, internal, 46, 214
Couldn't classify 429, 629
Sorry, prediction GlimmerHMM_glimmerT_62499-T1 fails validation.
(ATG)	 TG	133-214	GT	CAG
(ATG)	 AG	429-629	GT	AGG
-recovered GlimmerHMM_glimmerT_62499-T1, initial, 133, 214
add_exon() Sorry, GlimmerHMM_glimmerT_62499-T1 429-629-initial-1 is invalid.
-recovered GlimmerHMM_glimmerT_62499-T1, initial, 429, 629
-recovered GlimmerHMM_glimmerT_62499-T1, internal, 429, 629
Valid prediction for GeneMark_model.108964_t
Couldn't classify 46, 214
Sorry, prediction snap_scaffold_1147-snap.1-T1 fails validation.
(TTT)	 AG	46-214	GT	CAG
(ATG)	 AG	429-629	GT	AGG
(GGC)	 AG	721-798	GT	CAG
(AAT)	 AG	2991-3124	CT	AGC
add_exon() Sorry, snap_scaffold_1147-snap.1-T1 429-629-initial-1 is invalid.
-recovered snap_scaffold_1147-snap.1-T1, initial, 429, 629
-recovered snap_scaffold_1147-snap.1-T1, terminal, 2991, 3124
-recovered snap_scaffold_1147-snap.1-T1, internal, 46, 214
-recovered snap_scaffold_1147-snap.1-T1, internal, 429, 629
-recovered snap_scaffold_1147-snap.1-T1, internal, 721, 798
Couldn't classify 46, 214
Sorry, prediction GeneMark_model.108963_t fails validation.
(TTT)	 AG	46-214	GT	CAG
(ATG)	 AG	429-629	GT	AGG
(GGC)	 AG	721-790	GT	CGG
(AGA)	 AG	981-1203	GA	AAG
add_exon() Sorry, GeneMark_model.108963_t 429-629-initial-1 is invalid.
-recovered GeneMark_model.108963_t, initial, 429, 629
-recovered GeneMark_model.108963_t, terminal, 981, 1203
-recovered GeneMark_model.108963_t, internal, 46, 214
-recovered GeneMark_model.108963_t, internal, 429, 629
-recovered GeneMark_model.108963_t, internal, 721, 790
Couldn't classify 46, 214
Sorry, prediction Augustus_model.g41551.t1 fails validation.
(TTT)	 AG	46-214	GT	CAG
(ATG)	 AG	429-629	GT	AGG
(TGC)	 AG	782-864	AA	AGA
add_exon() Sorry, Augustus_model.g41551.t1 429-629-initial-1 is invalid.
-recovered Augustus_model.g41551.t1, initial, 429, 629
-recovered Augustus_model.g41551.t1, terminal, 782, 864
-recovered Augustus_model.g41551.t1, internal, 46, 214
-recovered Augustus_model.g41551.t1, internal, 429, 629

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

-building trellis in range 1 - 3134
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-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