-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_557

-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: -)Valid prediction for GlimmerHMM_glimmerT_60484-T1
Couldn't classify 5802, 5870
Sorry, prediction Augustus_model.g40039.t1 fails validation.
(ATG)	 GA	4160-4270	GT	AGG
(GTG)	 AG	4490-4662	GT	CAG
(ATT)	 AG	4914-4989	GT	AGG
(GTG)	 AG	5188-5361	GT	AGG
(CTG)	 AG	5533-5658	GT	AGG
(GTT)	 AG	5802-5870	GT	AGG
-recovered Augustus_model.g40039.t1, initial, 4160, 4270
-recovered Augustus_model.g40039.t1, internal, 4490, 4662
-recovered Augustus_model.g40039.t1, internal, 4914, 4989
-recovered Augustus_model.g40039.t1, internal, 5188, 5361
-recovered Augustus_model.g40039.t1, internal, 5533, 5658
-recovered Augustus_model.g40039.t1, internal, 5802, 5870
Couldn't classify 1, 196
Sorry, prediction Augustus_model.g40040.t1 fails validation.
(TCC)	 CA	1-196	GT	AGG
(GTT)	 AG	3914-3955	CC	AAC
-recovered Augustus_model.g40040.t1, terminal, 3914, 3955
Valid prediction for GlimmerHMM_glimmerT_60483-T1
Couldn't classify 4927, 4989
Couldn't classify 5802, 5867
Sorry, prediction pasa_asmbl_46563.p1 fails validation.
(AAG)	 AG	4927-4989	GT	AGG
(GTG)	 AG	5188-5361	GT	AGG
(CTG)	 AG	5533-5658	GT	AGG
(GTT)	 AG	5802-5867	GA	CCG
-recovered pasa_asmbl_46563.p1, internal, 4927, 4989
-recovered pasa_asmbl_46563.p1, internal, 5188, 5361
-recovered pasa_asmbl_46563.p1, internal, 5533, 5658
Couldn't classify 5802, 5870
Sorry, prediction snap_scaffold_557-snap.1-T1 fails validation.
(ATG)	 GA	4160-4270	GT	AGG
(GTG)	 AG	4490-4662	GT	CAG
(ATT)	 AG	4914-4989	GT	AGG
(GTG)	 AG	5188-5361	GT	AGG
(CTG)	 AG	5533-5658	GT	AGG
(GTT)	 AG	5802-5870	GT	AGG
-recovered snap_scaffold_557-snap.1-T1, initial, 4160, 4270
-recovered snap_scaffold_557-snap.1-T1, internal, 4490, 4662
-recovered snap_scaffold_557-snap.1-T1, internal, 4914, 4989
-recovered snap_scaffold_557-snap.1-T1, internal, 5188, 5361
-recovered snap_scaffold_557-snap.1-T1, internal, 5533, 5658
-recovered snap_scaffold_557-snap.1-T1, internal, 5802, 5870
Couldn't classify 20, 196
Sorry, prediction snap_scaffold_557-snap.2-T1 fails validation.
(GAT)	 AG	20-196	GT	AGG
(GAG)	 AG	3329-3352	AT	AAA
-recovered snap_scaffold_557-snap.2-T1, terminal, 3329, 3352
-recovered snap_scaffold_557-snap.2-T1, internal, 20, 196

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

-building trellis in range 1 - 5891
-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 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