-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1089

-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 15, 78
Couldn't classify 2732, 3124
Sorry, prediction GeneMark_model.108878_t fails validation.
(GCC)	 AG	15-78	GT	GGG
(ACA)	 AG	375-562	GT	ATG
(ACG)	 AG	719-775	GT	AGG
(GCC)	 AG	847-1024	GT	CTG
(GGT)	 AG	1194-1210	GT	AGG
(CCA)	 AG	1459-1736	GT	GAG
(GGT)	 AG	1825-2008	GT	CTG
(GCC)	 AG	2108-2126	GT	GGG
(AAG)	 AG	2324-2617	GT	GAG
(GGT)	 AG	2732-3124	GT	AGG
add_exon() Sorry, GeneMark_model.108878_t 1459-1736-terminal-2 is invalid.
-recovered GeneMark_model.108878_t, terminal, 1459, 1736
-recovered GeneMark_model.108878_t, internal, 15, 78
-recovered GeneMark_model.108878_t, internal, 375, 562
-recovered GeneMark_model.108878_t, internal, 719, 775
-recovered GeneMark_model.108878_t, internal, 847, 1024
-recovered GeneMark_model.108878_t, internal, 1194, 1210
-recovered GeneMark_model.108878_t, internal, 1459, 1736
-recovered GeneMark_model.108878_t, internal, 1825, 2008
-recovered GeneMark_model.108878_t, internal, 2108, 2126
-recovered GeneMark_model.108878_t, internal, 2324, 2617
-recovered GeneMark_model.108878_t, internal, 2732, 3124
Couldn't classify 2732, 3124
Sorry, prediction GlimmerHMM_glimmerT_62459-T1 fails validation.
(ATG)	 TC	1181-1210	GT	AGG
(CCA)	 AG	1459-1732	GT	CTG
(CTC)	 AG	2327-2617	GT	GAG
(GGT)	 AG	2732-3124	GT	AGG
-recovered GlimmerHMM_glimmerT_62459-T1, initial, 1181, 1210
-recovered GlimmerHMM_glimmerT_62459-T1, internal, 1459, 1732
-recovered GlimmerHMM_glimmerT_62459-T1, internal, 2327, 2617
-recovered GlimmerHMM_glimmerT_62459-T1, internal, 2732, 3124
Couldn't classify 1, 78
Couldn't classify 2732, 3124
Sorry, prediction Augustus_model.g41519.t1 fails validation.
(CCC)	 GG	1-78	GT	GGG
(ACA)	 AG	375-562	GT	ATG
(ACG)	 AG	719-775	GT	AGG
(GCC)	 AG	847-1024	GT	CTG
(ACC)	 AG	1424-1736	GT	GAG
(GGT)	 AG	1825-1930	GT	TGG
(GCC)	 AG	2108-2126	GT	GGG
(AAG)	 AG	2324-2617	GT	GAG
(GGT)	 AG	2732-3124	GT	AGG
add_exon() Sorry, Augustus_model.g41519.t1 1424-1736-terminal-3 is invalid.
-recovered Augustus_model.g41519.t1, terminal, 1424, 1736
-recovered Augustus_model.g41519.t1, internal, 375, 562
-recovered Augustus_model.g41519.t1, internal, 719, 775
-recovered Augustus_model.g41519.t1, internal, 847, 1024
-recovered Augustus_model.g41519.t1, internal, 1424, 1736
-recovered Augustus_model.g41519.t1, internal, 1825, 1930
-recovered Augustus_model.g41519.t1, internal, 2108, 2126
-recovered Augustus_model.g41519.t1, internal, 2324, 2617
-recovered Augustus_model.g41519.t1, internal, 2732, 3124
Couldn't classify 294, 562
Couldn't classify 2732, 3124
Sorry, prediction snap_scaffold_1089-snap.1-T1 fails validation.
(TCC)	 AG	294-562	GT	ATG
(ACG)	 AG	719-775	GT	AGG
(GCC)	 AG	847-1024	GT	CTG
(ACC)	 AG	1424-1736	GT	GAG
(GGT)	 AG	1825-1930	GT	TGG
(GCC)	 AG	2108-2126	GT	GGG
(AAG)	 AG	2324-2617	GT	GAG
(GGT)	 AG	2732-3124	GT	AGG
add_exon() Sorry, snap_scaffold_1089-snap.1-T1 1424-1736-terminal-3 is invalid.
-recovered snap_scaffold_1089-snap.1-T1, terminal, 1424, 1736
-recovered snap_scaffold_1089-snap.1-T1, internal, 294, 562
-recovered snap_scaffold_1089-snap.1-T1, internal, 719, 775
-recovered snap_scaffold_1089-snap.1-T1, internal, 847, 1024
-recovered snap_scaffold_1089-snap.1-T1, internal, 1424, 1736
-recovered snap_scaffold_1089-snap.1-T1, internal, 1825, 1930
-recovered snap_scaffold_1089-snap.1-T1, internal, 2108, 2126
-recovered snap_scaffold_1089-snap.1-T1, internal, 2324, 2617
-recovered snap_scaffold_1089-snap.1-T1, internal, 2732, 3124
Valid prediction for GlimmerHMM_glimmerT_62458-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: -)
-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 3322
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-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