-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1336

-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 2422, 2520
Sorry, prediction GeneMark_model.109218_t fails validation.
(ATG)	 TC	1701-1765	GT	AAG
(AGA)	 AG	1834-1842	GT	GAG
(TGA)	 AG	1868-1891	GT	GCG
(AGG)	 AG	1989-2117	GT	GGG
(AGA)	 AG	2211-2276	GC	GGG
(ACA)	 AG	2302-2310	GT	GAG
(AGT)	 AG	2332-2358	GT	GAG
(ACA)	 AG	2380-2400	GT	GAG
(ACA)	 AG	2422-2520	GT	CTG
-recovered GeneMark_model.109218_t, initial, 1701, 1765
-recovered GeneMark_model.109218_t, internal, 1834, 1842
-recovered GeneMark_model.109218_t, internal, 1868, 1891
-recovered GeneMark_model.109218_t, internal, 1989, 2117
-recovered GeneMark_model.109218_t, internal, 2211, 2276
-recovered GeneMark_model.109218_t, internal, 2302, 2310
-recovered GeneMark_model.109218_t, internal, 2332, 2358
-recovered GeneMark_model.109218_t, internal, 2380, 2400
-recovered GeneMark_model.109218_t, internal, 2422, 2520
Couldn't classify 36, 50
Sorry, prediction GeneMark_model.109216_t fails validation.
(AGA)	 AG	36-50	GT	CAG
(AGA)	 AG	76-84	GT	CAG
(AGA)	 AG	106-120	GT	CAG
(AGA)	 AG	142-188	GT	CAG
(AGA)	 AG	206-212	GT	CAG
(ACA)	 AG	236-268	GT	CAG
(AGA)	 AG	292-366	GT	CAG
(AGA)	 AG	392-460	GT	CAG
(AGA)	 AG	482-524	GA	GAG
-recovered GeneMark_model.109216_t, terminal, 482, 524
-recovered GeneMark_model.109216_t, internal, 36, 50
-recovered GeneMark_model.109216_t, internal, 76, 84
-recovered GeneMark_model.109216_t, internal, 106, 120
-recovered GeneMark_model.109216_t, internal, 142, 188
-recovered GeneMark_model.109216_t, internal, 206, 212
-recovered GeneMark_model.109216_t, internal, 236, 268
-recovered GeneMark_model.109216_t, internal, 292, 366
-recovered GeneMark_model.109216_t, internal, 392, 460
Couldn't classify 1302, 1409
Couldn't classify 2211, 2310
Sorry, prediction snap_scaffold_1336-snap.1-T1 fails validation.
(GCT)	 AG	1302-1409	GT	ATG
(GAT)	 AG	1981-2117	GT	GGG
(AGA)	 AG	2211-2310	GT	GAG
-recovered snap_scaffold_1336-snap.1-T1, internal, 1302, 1409
-recovered snap_scaffold_1336-snap.1-T1, internal, 1981, 2117
-recovered snap_scaffold_1336-snap.1-T1, internal, 2211, 2310

-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.109217_t
Valid prediction for GlimmerHMM_glimmerT_62589-T1

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

-building trellis in range 1 - 2628
-exon list size: 53


building trellis

1.8    
3.6    
5.5    
7.3    
9.1    
10.9    
12.7    
14.5    
16.4    
18.2    
20.0    
21.8    
23.6    
25.5    
27.3    
29.1    
30.9    
32.7    
34.5    
36.4    
38.2    
40.0    
41.8    
43.6    
45.5    
47.3    
49.1    
50.9    
52.7    
54.5    
56.4    
58.2    
60.0    
61.8    
63.6    
65.5    
67.3    
69.1    
70.9    
72.7    
74.5    
76.4    
78.2    
80.0    
81.8    
83.6    
85.5    
87.3    
89.1    
90.9    
92.7    
94.5    
96.4    
98.2    
-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