-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_653

-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.108138_t
Valid prediction for GeneMark_model.108136_t
Valid prediction for snap_scaffold_653-snap.4-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: -)Valid prediction for GeneMark_model.108137_t
Valid prediction for Augustus_model.g41273.t1
Valid prediction for GlimmerHMM_glimmerT_62089-T1
Valid prediction for CodingQuarry_transcript_55334-T1
Valid prediction for GlimmerHMM_glimmerT_62088-T1
Couldn't classify 876, 1041
Sorry, prediction GlimmerHMM_glimmerT_62090-T1 fails validation.
(CTT)	 AG	876-1041	GT	CAG
(CCG)	 AG	1895-2056	AC	GAA
-recovered GlimmerHMM_glimmerT_62090-T1, terminal, 1895, 2056
-recovered GlimmerHMM_glimmerT_62090-T1, internal, 876, 1041
Couldn't classify 4922, 5081
Sorry, prediction snap_scaffold_653-snap.1-T1 fails validation.
(ATG)	 CT	4518-4635	GT	CAG
(GTG)	 AG	4815-4878	GT	GAG
(AGG)	 AG	4922-5081	GT	ATG
-recovered snap_scaffold_653-snap.1-T1, initial, 4518, 4635
-recovered snap_scaffold_653-snap.1-T1, internal, 4815, 4878
-recovered snap_scaffold_653-snap.1-T1, internal, 4922, 5081
Valid prediction for snap_scaffold_653-snap.2-T1
Valid prediction for snap_scaffold_653-snap.3-T1
Couldn't classify 4937, 5081
Sorry, prediction GeneMark_model.108135_t fails validation.
(ATG)	 CT	4518-4635	GT	CAG
(GTG)	 AG	4815-4917	GT	CTG
(GGA)	 AG	4937-5081	GT	ATG
-recovered GeneMark_model.108135_t, initial, 4518, 4635
-recovered GeneMark_model.108135_t, internal, 4815, 4917
-recovered GeneMark_model.108135_t, internal, 4937, 5081

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

-building trellis in range 1 - 5120
-exon list size: 39


building trellis

2.4    
4.9    
7.3    
9.8    
12.2    
14.6    
17.1    
19.5    
22.0    
24.4    
26.8    
29.3    
31.7    
34.1    
36.6    
39.0    
41.5    
43.9    
46.3    
48.8    
51.2    
53.7    
56.1    
58.5    
61.0    
63.4    
65.9    
68.3    
70.7    
73.2    
75.6    
78.0    
80.5    
82.9    
85.4    
87.8    
90.2    
92.7    
95.1    
97.6    
-found 3 predictions from path traversal

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