-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1629

-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, 172
Couldn't classify 2085, 2094
Sorry, prediction GeneMark_model.109556_t fails validation.
(GGG)	 AG	15-172	GT	GTG
(TCG)	 AG	395-527	GT	GGG
(GGG)	 AG	557-643	GT	GAG
(TGA)	 AG	682-687	GT	GTG
(GGA)	 AG	814-828	GT	TTG
(TGA)	 AG	904-930	GT	AGG
(AGT)	 AG	956-970	GT	GGG
(AGG)	 AG	1004-1054	GT	AGG
(GGA)	 AG	1078-1104	GT	AAG
(GGT)	 AG	1278-1376	GT	AAG
(GGG)	 AG	1850-1861	GT	GAG
(AGG)	 AG	1886-1900	GT	GGG
(AGC)	 AG	1926-1952	GT	GTG
(AGA)	 AG	1974-1985	GT	GAG
(TGG)	 AG	2007-2063	GT	GTG
(AGT)	 AG	2085-2094	GT	GAG
-recovered GeneMark_model.109556_t, internal, 15, 172
-recovered GeneMark_model.109556_t, internal, 395, 527
-recovered GeneMark_model.109556_t, internal, 557, 643
-recovered GeneMark_model.109556_t, internal, 682, 687
-recovered GeneMark_model.109556_t, internal, 814, 828
-recovered GeneMark_model.109556_t, internal, 904, 930
-recovered GeneMark_model.109556_t, internal, 956, 970
-recovered GeneMark_model.109556_t, internal, 1004, 1054
-recovered GeneMark_model.109556_t, internal, 1078, 1104
-recovered GeneMark_model.109556_t, internal, 1278, 1376
-recovered GeneMark_model.109556_t, internal, 1850, 1861
-recovered GeneMark_model.109556_t, internal, 1886, 1900
-recovered GeneMark_model.109556_t, internal, 1926, 1952
-recovered GeneMark_model.109556_t, internal, 1974, 1985
-recovered GeneMark_model.109556_t, internal, 2007, 2063
-recovered GeneMark_model.109556_t, internal, 2085, 2094

-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 1952, 2080
Sorry, prediction Augustus_model.g41769.t1 fails validation.
(ATG)	 AC	392-479	GT	GAG
(CGT)	 AG	768-899	GT	GAG
(AGT)	 AG	1608-1736	GT	GGG
(GTT)	 AG	1952-2080	GT	GGG
-recovered Augustus_model.g41769.t1, initial, 392, 479
add_exon() Sorry, Augustus_model.g41769.t1 768-899-terminal-1 is invalid.
-recovered Augustus_model.g41769.t1, terminal, 768, 899
-recovered Augustus_model.g41769.t1, internal, 768, 899
-recovered Augustus_model.g41769.t1, internal, 1608, 1736
-recovered Augustus_model.g41769.t1, internal, 1952, 2080
Couldn't classify 768, 899
Couldn't classify 1952, 2080
Sorry, prediction snap_scaffold_1629-snap.1-T1 fails validation.
(CGT)	 AG	768-899	GT	GAG
(AGT)	 AG	1608-1736	GT	GGG
(GTT)	 AG	1952-2080	GT	GGG
add_exon() Sorry, snap_scaffold_1629-snap.1-T1 768-899-terminal-1 is invalid.
-recovered snap_scaffold_1629-snap.1-T1, terminal, 768, 899
-recovered snap_scaffold_1629-snap.1-T1, internal, 768, 899
-recovered snap_scaffold_1629-snap.1-T1, internal, 1608, 1736
-recovered snap_scaffold_1629-snap.1-T1, internal, 1952, 2080
Couldn't classify 768, 899
Sorry, prediction GlimmerHMM_glimmerT_62750-T1 fails validation.
(CGT)	 AG	768-899	GT	GAG
(AGT)	 AG	1608-2029	CC	GAC
add_exon() Sorry, GlimmerHMM_glimmerT_62750-T1 768-899-terminal-1 is invalid.
-recovered GlimmerHMM_glimmerT_62750-T1, terminal, 768, 899
-recovered GlimmerHMM_glimmerT_62750-T1, terminal, 1608, 2029
-recovered GlimmerHMM_glimmerT_62750-T1, internal, 768, 899

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

-building trellis in range 1 - 2119
-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 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