-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_541

-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: +)Couldn't classify 1790, 1855
Couldn't classify 5631, 5751
Sorry, prediction snap_scaffold_541-snap.1-T1 fails validation.
(GCA)	 AG	1790-1855	GT	AGG
(AGA)	 AG	2071-2152	GT	ATG
(GGA)	 AG	5209-5480	GT	CGG
(CGG)	 AG	5631-5751	GT	TGG
-recovered snap_scaffold_541-snap.1-T1, terminal, 1790, 1855
-recovered snap_scaffold_541-snap.1-T1, internal, 1790, 1855
-recovered snap_scaffold_541-snap.1-T1, internal, 2071, 2152
-recovered snap_scaffold_541-snap.1-T1, internal, 5209, 5480
-recovered snap_scaffold_541-snap.1-T1, internal, 5631, 5751
Valid prediction for GeneMark_model.107898_t

-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 5526, 5537
Sorry, prediction GeneMark_model.107897_t fails validation.
(ATG)	 TC	296-436	GT	TGG
(GTG)	 AG	673-833	GT	CGG
(AGA)	 AG	1527-1592	GT	AGG
(AGA)	 AG	1621-1749	GT	GAG
(AGG)	 AG	1771-1803	GT	GAG
(AGA)	 AG	2935-3090	GT	AGG
(GAA)	 AG	3112-3120	GT	GAG
(AGG)	 AG	3142-3159	GT	GAG
(AAA)	 AG	3515-3610	GT	AGG
(AGG)	 AG	4973-4981	GT	GAG
(AGG)	 AG	5012-5020	GT	GAG
(TAG)	 AG	5048-5059	GT	GAG
(TAG)	 AG	5082-5093	GT	GAG
(TAG)	 AG	5121-5126	GT	GGG
(AGG)	 AG	5150-5158	GT	GAG
(AGG)	 AG	5189-5197	GT	GAG
(TAG)	 AG	5220-5231	GT	GAG
(TAG)	 AG	5259-5270	GT	GAG
(TAG)	 AG	5297-5308	GT	GAG
(TAG)	 AG	5331-5342	GT	GAG
(TAG)	 AG	5370-5381	GT	GAG
(TAG)	 AG	5409-5420	GT	GAG
(TAG)	 AG	5448-5459	GT	GAG
(TAG)	 AG	5487-5498	GT	GAG
(TAG)	 AG	5526-5537	GT	GAG
-recovered GeneMark_model.107897_t, initial, 296, 436
-recovered GeneMark_model.107897_t, internal, 673, 833
-recovered GeneMark_model.107897_t, internal, 1527, 1592
-recovered GeneMark_model.107897_t, internal, 1621, 1749
-recovered GeneMark_model.107897_t, internal, 1771, 1803
-recovered GeneMark_model.107897_t, internal, 2935, 3090
-recovered GeneMark_model.107897_t, internal, 3112, 3120
-recovered GeneMark_model.107897_t, internal, 3142, 3159
-recovered GeneMark_model.107897_t, internal, 3515, 3610
-recovered GeneMark_model.107897_t, internal, 4973, 4981
-recovered GeneMark_model.107897_t, internal, 5012, 5020
-recovered GeneMark_model.107897_t, internal, 5048, 5059
-recovered GeneMark_model.107897_t, internal, 5082, 5093
-recovered GeneMark_model.107897_t, internal, 5121, 5126
-recovered GeneMark_model.107897_t, internal, 5150, 5158
-recovered GeneMark_model.107897_t, internal, 5189, 5197
-recovered GeneMark_model.107897_t, internal, 5220, 5231
-recovered GeneMark_model.107897_t, internal, 5259, 5270
-recovered GeneMark_model.107897_t, internal, 5297, 5308
-recovered GeneMark_model.107897_t, internal, 5331, 5342
-recovered GeneMark_model.107897_t, internal, 5370, 5381
-recovered GeneMark_model.107897_t, internal, 5409, 5420
-recovered GeneMark_model.107897_t, internal, 5448, 5459
-recovered GeneMark_model.107897_t, internal, 5487, 5498
-recovered GeneMark_model.107897_t, internal, 5526, 5537
Couldn't classify 221, 436
Sorry, prediction Augustus_model.g41192.t1 fails validation.
(AAA)	 AG	221-436	GT	TGG
(GTG)	 AG	673-837	GT	GAG
-recovered Augustus_model.g41192.t1, terminal, 673, 837
-recovered Augustus_model.g41192.t1, internal, 221, 436
-recovered Augustus_model.g41192.t1, internal, 673, 837
Couldn't classify 221, 436
Sorry, prediction GlimmerHMM_glimmerT_61971-T1 fails validation.
(AAA)	 AG	221-436	GT	TGG
(GTG)	 AG	673-837	GT	GAG
-recovered GlimmerHMM_glimmerT_61971-T1, terminal, 673, 837
-recovered GlimmerHMM_glimmerT_61971-T1, internal, 221, 436
-recovered GlimmerHMM_glimmerT_61971-T1, internal, 673, 837

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

-building trellis in range 1 - 6000
-exon list size: 55


building trellis

1.8    
3.5    
5.3    
7.0    
8.8    
10.5    
12.3    
14.0    
15.8    
17.5    
19.3    
21.1    
22.8    
24.6    
26.3    
28.1    
29.8    
31.6    
33.3    
35.1    
36.8    
38.6    
40.4    
42.1    
43.9    
45.6    
47.4    
49.1    
50.9    
52.6    
54.4    
56.1    
57.9    
59.6    
61.4    
63.2    
64.9    
66.7    
68.4    
70.2    
71.9    
73.7    
75.4    
77.2    
78.9    
80.7    
82.5    
84.2    
86.0    
87.7    
89.5    
91.2    
93.0    
94.7    
96.5    
98.2    
-found 2 predictions from path traversal

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