-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_646

-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 4683, 4826
Sorry, prediction GeneMark_model.108122_t fails validation.
(ATG)	 AA	4588-4595	GT	TGG
(GGA)	 AG	4683-4826	GT	GCG
-recovered GeneMark_model.108122_t, initial, 4588, 4595
-recovered GeneMark_model.108122_t, internal, 4683, 4826
Valid prediction for GlimmerHMM_glimmerT_62080-T1
add_exon() Sorry, GlimmerHMM_glimmerT_62080-T1 328-505-terminal-1 is invalid.
Valid prediction for CodingQuarry_transcript_55331-T1
Valid prediction for GeneMark_model.108123_t
add_exon() Sorry, GeneMark_model.108123_t 333-505-terminal-1 is invalid.
Couldn't classify 328, 501
Sorry, prediction snap_scaffold_646-snap.2-T1 fails validation.
(CGT)	 AG	328-501	GT	GCG
(AAT)	 AG	712-827	GT	AGG
(TGT)	 AG	951-1120	TA	AGT
-recovered snap_scaffold_646-snap.2-T1, terminal, 951, 1120
-recovered snap_scaffold_646-snap.2-T1, internal, 328, 501
-recovered snap_scaffold_646-snap.2-T1, internal, 712, 827
Valid prediction for GlimmerHMM_glimmerT_62079-T1
Couldn't classify 328, 501
Couldn't classify 5011, 5126
Sorry, prediction Augustus_model.g41267.t1 fails validation.
(CGT)	 AG	328-501	GT	GCG
(AAT)	 AG	712-827	GT	AGG
(TGT)	 AG	951-1119	GT	TAG
(CTA)	 AG	1402-1471	GT	AAG
(ATG)	 AG	1663-1717	GT	TGG
(GAC)	 AG	3900-3917	GT	TGG
(TGA)	 AG	4075-4095	GT	GCG
(GAG)	 AG	4192-4224	GT	AAG
(CTG)	 AG	4347-4373	GT	CAG
(CTG)	 AG	4523-4549	GT	CAG
(AGT)	 AG	4658-4826	GT	GCG
(AAT)	 AG	5011-5126	GT	AGG
-recovered Augustus_model.g41267.t1, initial, 1663, 1717
-recovered Augustus_model.g41267.t1, internal, 328, 501
-recovered Augustus_model.g41267.t1, internal, 712, 827
-recovered Augustus_model.g41267.t1, internal, 951, 1119
-recovered Augustus_model.g41267.t1, internal, 1402, 1471
-recovered Augustus_model.g41267.t1, internal, 1663, 1717
-recovered Augustus_model.g41267.t1, internal, 3900, 3917
-recovered Augustus_model.g41267.t1, internal, 4075, 4095
-recovered Augustus_model.g41267.t1, internal, 4192, 4224
-recovered Augustus_model.g41267.t1, internal, 4347, 4373
-recovered Augustus_model.g41267.t1, internal, 4523, 4549
-recovered Augustus_model.g41267.t1, internal, 4658, 4826
-recovered Augustus_model.g41267.t1, internal, 5011, 5126
Couldn't classify 35, 86
Sorry, prediction pasa_asmbl_49432.p1 fails validation.
(AAT)	 TA	35-86	GT	AAG
(CTG)	 AG	198-224	GT	CAG
(AGT)	 AG	333-501	GT	GCG
(AAT)	 AG	712-827	GT	AGG
(TGT)	 AG	951-1119	GT	TAG
(CTA)	 AG	1402-1513	AC	AAA
-recovered pasa_asmbl_49432.p1, terminal, 1402, 1513
-recovered pasa_asmbl_49432.p1, internal, 198, 224
-recovered pasa_asmbl_49432.p1, internal, 333, 501
-recovered pasa_asmbl_49432.p1, internal, 712, 827
-recovered pasa_asmbl_49432.p1, internal, 951, 1119
Valid prediction for snap_scaffold_646-snap.1-T1

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

-building trellis in range 1 - 5176
-exon list size: 35


building trellis

2.7    
5.4    
8.1    
10.8    
13.5    
16.2    
18.9    
21.6    
24.3    
27.0    
29.7    
32.4    
35.1    
37.8    
40.5    
43.2    
45.9    
48.6    
51.4    
54.1    
56.8    
59.5    
62.2    
64.9    
67.6    
70.3    
73.0    
75.7    
78.4    
81.1    
83.8    
86.5    
89.2    
91.9    
94.6    
97.3    
-found 2 predictions from path traversal

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