-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_405

-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_61806-T1
Couldn't classify 1894, 2055
Couldn't classify 2909, 2988
Sorry, prediction pasa_asmbl_43652.p1 fails validation.
(GTC)	 AG	1894-2055	GT	TGG
(AGG)	 AG	2296-2461	GT	AGG
(ATG)	 AG	2909-2988	CC	GAC
-recovered pasa_asmbl_43652.p1, internal, 1894, 2055
-recovered pasa_asmbl_43652.p1, internal, 2296, 2461
Couldn't classify 1894, 2055
Sorry, prediction snap_scaffold_405-snap.1-T1 fails validation.
(GTC)	 AG	1894-2055	GT	TGG
(AGG)	 AG	2296-2673	GG	GAG
-recovered snap_scaffold_405-snap.1-T1, terminal, 2296, 2673
-recovered snap_scaffold_405-snap.1-T1, internal, 1894, 2055
Valid prediction for GeneMark_model.107546_t
Couldn't classify 4230, 4429
Sorry, prediction snap_scaffold_405-snap.2-T1 fails validation.
(ATG)	 GG	2685-2709	GT	GGG
(ATG)	 AG	2909-2982	GT	AGG
(ACA)	 AG	3764-3960	GT	CAG
(CCA)	 AG	4230-4429	GT	CAG
-recovered snap_scaffold_405-snap.2-T1, initial, 2685, 2709
add_exon() Sorry, snap_scaffold_405-snap.2-T1 2909-2982-initial-1 is invalid.
-recovered snap_scaffold_405-snap.2-T1, initial, 2909, 2982
-recovered snap_scaffold_405-snap.2-T1, internal, 2909, 2982
-recovered snap_scaffold_405-snap.2-T1, internal, 3764, 3960
-recovered snap_scaffold_405-snap.2-T1, internal, 4230, 4429
Couldn't classify 1894, 2055
Sorry, prediction Augustus_model.g41078.t1 fails validation.
(GTC)	 AG	1894-2055	GT	TGG
(AGG)	 AG	2296-2461	GT	AGG
(ATG)	 AG	2909-2982	GT	AGG
(AAC)	 AG	3998-4054	GC	GAG
add_exon() Sorry, Augustus_model.g41078.t1 2909-2982-initial-1 is invalid.
-recovered Augustus_model.g41078.t1, initial, 2909, 2982
-recovered Augustus_model.g41078.t1, terminal, 3998, 4054
-recovered Augustus_model.g41078.t1, internal, 1894, 2055
-recovered Augustus_model.g41078.t1, internal, 2296, 2461
-recovered Augustus_model.g41078.t1, internal, 2909, 2982
-recovered Augustus_model.g41078.t1, internal, 3998, 4054

-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 367, 450
Sorry, prediction GeneMark_model.107547_t fails validation.
(GGA)	 AG	367-450	GT	ATG
(GGA)	 AG	1469-1586	GA	GAG
-recovered GeneMark_model.107547_t, terminal, 1469, 1586
-recovered GeneMark_model.107547_t, internal, 367, 450
Valid prediction for GeneMark_model.107545_t

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

-building trellis in range 1 - 7243
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-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