-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_999

-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 590, 670
Sorry, prediction GlimmerHMM_glimmerT_62398-T1 fails validation.
(CCT)	 AG	590-670	GT	ACG
(GTG)	 AG	1495-1653	GT	GAG
(AGT)	 AG	2066-2275	GT	GAG
(ATA)	 AG	2908-3242	TG	AGT
-recovered GlimmerHMM_glimmerT_62398-T1, terminal, 2908, 3242
-recovered GlimmerHMM_glimmerT_62398-T1, internal, 590, 670
-recovered GlimmerHMM_glimmerT_62398-T1, internal, 1495, 1653
-recovered GlimmerHMM_glimmerT_62398-T1, internal, 2066, 2275
Couldn't classify 3569, 3630
Sorry, prediction Augustus_model.g41477.t1 fails validation.
(ATG)	 AG	642-687	GT	AGG
(GTG)	 AG	1495-1653	GT	GAG
(ATT)	 AG	2338-2511	GT	TGG
(ATA)	 AG	2908-3237	GT	AGG
(CCA)	 AG	3569-3630		CC
-recovered Augustus_model.g41477.t1, initial, 642, 687
-recovered Augustus_model.g41477.t1, internal, 642, 687
-recovered Augustus_model.g41477.t1, internal, 1495, 1653
-recovered Augustus_model.g41477.t1, internal, 2338, 2511
-recovered Augustus_model.g41477.t1, internal, 2908, 3237
Couldn't classify 590, 687
Couldn't classify 2908, 3237
Sorry, prediction snap_scaffold_999-snap.1-T1 fails validation.
(CCT)	 AG	590-687	GT	AGG
(AGG)	 AG	888-913	GT	GGG
(GTG)	 AG	1495-1653	GT	GAG
(ATT)	 AG	2338-2511	GT	TGG
(ATA)	 AG	2908-3237	GT	AGG
-recovered snap_scaffold_999-snap.1-T1, internal, 590, 687
-recovered snap_scaffold_999-snap.1-T1, internal, 888, 913
-recovered snap_scaffold_999-snap.1-T1, internal, 1495, 1653
-recovered snap_scaffold_999-snap.1-T1, internal, 2338, 2511
-recovered snap_scaffold_999-snap.1-T1, internal, 2908, 3237
Couldn't classify 590, 687
Couldn't classify 3569, 3620
Sorry, prediction GeneMark_model.108742_t fails validation.
(CCT)	 AG	590-687	GT	AGG
(AGG)	 AG	888-913	GT	GGG
(GTG)	 AG	1495-1653	GT	GAG
(AAG)	 AG	1751-1769	GT	AGG
(GGG)	 AG	1796-1804	GT	AGG
(GTG)	 AG	1843-1889	GT	AGG
(AGT)	 AG	2203-2239	GT	GAG
(GGC)	 AG	2283-2384	GT	GAG
(ATG)	 AG	2597-2637	GT	AGG
(ATA)	 AG	2908-3210	GT	GAG
(CCA)	 AG	3569-3620	GC	CTG
-recovered GeneMark_model.108742_t, initial, 2597, 2637
-recovered GeneMark_model.108742_t, internal, 590, 687
-recovered GeneMark_model.108742_t, internal, 888, 913
-recovered GeneMark_model.108742_t, internal, 1495, 1653
-recovered GeneMark_model.108742_t, internal, 1751, 1769
-recovered GeneMark_model.108742_t, internal, 1796, 1804
-recovered GeneMark_model.108742_t, internal, 1843, 1889
-recovered GeneMark_model.108742_t, internal, 2203, 2239
-recovered GeneMark_model.108742_t, internal, 2283, 2384
-recovered GeneMark_model.108742_t, internal, 2597, 2637
-recovered GeneMark_model.108742_t, internal, 2908, 3210
-recovered GeneMark_model.108742_t, internal, 3569, 3620

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

-building trellis in range 1 - 3630
-exon list size: 37


building trellis

2.6    
5.1    
7.7    
10.3    
12.8    
15.4    
17.9    
20.5    
23.1    
25.6    
28.2    
30.8    
33.3    
35.9    
38.5    
41.0    
43.6    
46.2    
48.7    
51.3    
53.8    
56.4    
59.0    
61.5    
64.1    
66.7    
69.2    
71.8    
74.4    
76.9    
79.5    
82.1    
84.6    
87.2    
89.7    
92.3    
94.9    
97.4    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support