-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_558

-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_61988-T1

-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 130, 257
Sorry, prediction Augustus_model.g41204.t1 fails validation.
(TAC)	 AG	130-257	GT	AGG
(GGG)	 AG	621-865	GG	GAG
-recovered Augustus_model.g41204.t1, terminal, 621, 865
-recovered Augustus_model.g41204.t1, internal, 130, 257
Valid prediction for snap_scaffold_558-snap.2-T1
Couldn't classify 5343, 5506
Sorry, prediction GeneMark_model.107928_t fails validation.
(ATG)	 CT	2640-2818	GT	AGG
(ACT)	 AG	3538-3665	GT	AGG
(CTC)	 AG	4021-4145	GT	AGG
(GTG)	 AG	4276-4347	GT	GGG
(GTC)	 AG	5343-5506	GT	AGG
-recovered GeneMark_model.107928_t, initial, 2640, 2818
-recovered GeneMark_model.107928_t, internal, 3538, 3665
-recovered GeneMark_model.107928_t, internal, 4021, 4145
-recovered GeneMark_model.107928_t, internal, 4276, 4347
-recovered GeneMark_model.107928_t, internal, 5343, 5506
Couldn't classify 23, 54
Sorry, prediction GeneMark_model.107929_t fails validation.
(GAT)	 AG	23-54	GT	GGG
(GAC)	 AG	181-257	GT	AGG
(GGG)	 AG	621-655	GT	TGG
(CGC)	 AG	744-993	GA	AGG
-recovered GeneMark_model.107929_t, terminal, 744, 993
-recovered GeneMark_model.107929_t, internal, 23, 54
-recovered GeneMark_model.107929_t, internal, 181, 257
-recovered GeneMark_model.107929_t, internal, 621, 655
Valid prediction for GlimmerHMM_glimmerT_61987-T1
Couldn't classify 5746, 5857
Sorry, prediction Augustus_model.g41203.t1 fails validation.
(ATG)	 TC	2340-2349	GT	ACG
(ACG)	 AG	2455-2529	GT	CAG
(TGC)	 AG	2626-2818	GT	AGG
(GGA)	 AG	3580-3665	GT	AGG
(CTC)	 AG	4021-4145	GT	AGG
(GTG)	 AG	4276-4347	GT	GGG
(GTC)	 AG	5343-5506	GT	AGG
(GTT)	 AG	5746-5857	GT	AGG
-recovered Augustus_model.g41203.t1, initial, 2340, 2349
-recovered Augustus_model.g41203.t1, internal, 2455, 2529
-recovered Augustus_model.g41203.t1, internal, 2626, 2818
-recovered Augustus_model.g41203.t1, internal, 3580, 3665
-recovered Augustus_model.g41203.t1, internal, 4021, 4145
-recovered Augustus_model.g41203.t1, internal, 4276, 4347
-recovered Augustus_model.g41203.t1, internal, 5343, 5506
-recovered Augustus_model.g41203.t1, internal, 5746, 5857
Couldn't classify 5343, 5506
Sorry, prediction snap_scaffold_558-snap.1-T1 fails validation.
(ATG)	 TC	2340-2349	GT	ACG
(ACG)	 AG	2455-2529	GT	CAG
(TGC)	 AG	2626-2818	GT	AGG
(GGA)	 AG	3580-3665	GT	AGG
(CAA)	 AG	4027-4145	GT	AGG
(GTG)	 AG	4276-4347	GT	GGG
(GTC)	 AG	5343-5506	GT	AGG
-recovered snap_scaffold_558-snap.1-T1, initial, 2340, 2349
-recovered snap_scaffold_558-snap.1-T1, internal, 2455, 2529
-recovered snap_scaffold_558-snap.1-T1, internal, 2626, 2818
-recovered snap_scaffold_558-snap.1-T1, internal, 3580, 3665
-recovered snap_scaffold_558-snap.1-T1, internal, 4027, 4145
-recovered snap_scaffold_558-snap.1-T1, internal, 4276, 4347
-recovered snap_scaffold_558-snap.1-T1, internal, 5343, 5506

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

-building trellis in range 1 - 5869
-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
GOT 5prime partial gene.

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