-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_231

-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 GeneMark_model.107008_t
Couldn't classify 9053, 9143
Sorry, prediction snap_scaffold_231-snap.2-T1 fails validation.
(ATG)	 TG	7140-7270	GT	CAG
(GAG)	 AG	8656-8787	GT	GGG
(GCG)	 AG	9053-9143	GT	ACG
-recovered snap_scaffold_231-snap.2-T1, initial, 7140, 7270
-recovered snap_scaffold_231-snap.2-T1, internal, 8656, 8787
-recovered snap_scaffold_231-snap.2-T1, internal, 9053, 9143

-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_61543-T1
Couldn't classify 11, 103
Sorry, prediction GeneMark_model.107009_t fails validation.
(CCA)	 AG	11-103	GT	AGG
(GAT)	 AG	131-207	GT	AGG
(TCC)	 AG	519-640	GT	GAG
-recovered GeneMark_model.107009_t, terminal, 519, 640
-recovered GeneMark_model.107009_t, internal, 11, 103
-recovered GeneMark_model.107009_t, internal, 131, 207
-recovered GeneMark_model.107009_t, internal, 519, 640
Valid prediction for snap_scaffold_231-snap.1-T1
Valid prediction for GeneMark_model.107007_t
Valid prediction for GlimmerHMM_glimmerT_61544-T1
Valid prediction for Augustus_model.g40928.t1
Couldn't classify 5158, 5202
Sorry, prediction pasa_asmbl_31989.p1 fails validation.
(GAC)	 GA	5158-5202	GT	AGG
(GAG)	 AG	5346-5473	GT	AAG
(GTA)	 AG	5692-5851	CA	AAC
-recovered pasa_asmbl_31989.p1, terminal, 5692, 5851
-recovered pasa_asmbl_31989.p1, internal, 5346, 5473
Couldn't classify 8745, 8796
Sorry, prediction GeneMark_model.107006_t fails validation.
(ATG)	 AC	8573-8577	GT	GTG
(ACA)	 AG	8607-8651	GT	ATG
(GCA)	 AG	8677-8715	GT	AAG
(AAA)	 AG	8745-8796	GT	ATG
-recovered GeneMark_model.107006_t, initial, 8573, 8577
-recovered GeneMark_model.107006_t, internal, 8607, 8651
-recovered GeneMark_model.107006_t, internal, 8677, 8715
-recovered GeneMark_model.107006_t, internal, 8745, 8796
Valid prediction for GlimmerHMM_glimmerT_61541-T1
Valid prediction for GlimmerHMM_glimmerT_61542-T1
Valid prediction for Augustus_model.g40929.t1

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

-building trellis in range 1 - 9289
-exon list size: 41


building trellis

2.3    
4.7    
7.0    
9.3    
11.6    
14.0    
16.3    
18.6    
20.9    
23.3    
25.6    
27.9    
30.2    
32.6    
34.9    
37.2    
39.5    
41.9    
44.2    
46.5    
48.8    
51.2    
53.5    
55.8    
58.1    
60.5    
62.8    
65.1    
67.4    
69.8    
72.1    
74.4    
76.7    
79.1    
81.4    
83.7    
86.0    
88.4    
90.7    
93.0    
95.3    
97.7    
-found 3 predictions from path traversal

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