-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_139

-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 snap_scaffold_139-snap.3-T1
Couldn't classify 12404, 12494
Sorry, prediction snap_scaffold_139-snap.4-T1 fails validation.
(ATG)	 AG	11527-11655	GT	AGG
(GTT)	 AG	11744-11920	GT	ACG
(CTT)	 AG	12006-12151	GT	AAG
(GAA)	 AG	12404-12494	GT	AGG
-recovered snap_scaffold_139-snap.4-T1, initial, 11527, 11655
-recovered snap_scaffold_139-snap.4-T1, internal, 11527, 11655
-recovered snap_scaffold_139-snap.4-T1, internal, 11744, 11920
-recovered snap_scaffold_139-snap.4-T1, internal, 12006, 12151
-recovered snap_scaffold_139-snap.4-T1, internal, 12404, 12494
Valid prediction for snap_scaffold_139-snap.2-T1
Couldn't classify 12404, 12494
Sorry, prediction GlimmerHMM_glimmerT_59873-T1 fails validation.
(ATG)	 TG	9876-9927	GT	CCG
(ATG)	 AG	10704-10852	GT	TGG
(GAG)	 AG	11211-11338	GT	GAG
(CAA)	 AG	11466-11655	GT	AGG
(GTT)	 AG	11744-11920	GT	ACG
(CTT)	 AG	12006-12151	GT	AAG
(GAA)	 AG	12404-12494	GT	AGG
-recovered GlimmerHMM_glimmerT_59873-T1, initial, 9876, 9927
add_exon() Sorry, GlimmerHMM_glimmerT_59873-T1 10704-10852-initial-1 is invalid.
-recovered GlimmerHMM_glimmerT_59873-T1, initial, 10704, 10852
-recovered GlimmerHMM_glimmerT_59873-T1, internal, 10704, 10852
-recovered GlimmerHMM_glimmerT_59873-T1, internal, 11211, 11338
-recovered GlimmerHMM_glimmerT_59873-T1, internal, 11466, 11655
-recovered GlimmerHMM_glimmerT_59873-T1, internal, 11744, 11920
-recovered GlimmerHMM_glimmerT_59873-T1, internal, 12006, 12151
-recovered GlimmerHMM_glimmerT_59873-T1, internal, 12404, 12494
Valid prediction for Augustus_model.g39661.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 GlimmerHMM_glimmerT_59872-T1
Valid prediction for GlimmerHMM_glimmerT_59871-T1
Valid prediction for snap_scaffold_139-snap.1-T1
Valid prediction for Augustus_model.g39660.t1

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

-building trellis in range 1 - 13002
-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