-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1216

-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: +)Valid prediction for GlimmerHMM_glimmerT_62528-T1
Couldn't classify 410, 576
Sorry, prediction snap_scaffold_1216-snap.1-T1 fails validation.
(TCA)	 AG	410-576	GT	CGG
(GCC)	 AG	1395-1429	CC	AGC
-recovered snap_scaffold_1216-snap.1-T1, terminal, 1395, 1429
-recovered snap_scaffold_1216-snap.1-T1, internal, 410, 576
Couldn't classify 435, 619
Couldn't classify 2311, 2324
Sorry, prediction GeneMark_model.109044_t fails validation.
(AGG)	 AG	435-619	GT	GGG
(TCC)	 AG	1815-1830	GT	GGG
(GAG)	 AG	1854-1868	GT	GAG
(GGT)	 AG	1899-1952	GT	GAG
(GAG)	 AG	1981-1986	GT	GGG
(GGA)	 AG	2015-2029	GT	AGG
(AGG)	 AG	2055-2072	GT	AGG
(GGA)	 AG	2097-2204	GT	GGG
(GGT)	 AG	2226-2255	GT	GGG
(GAT)	 AG	2276-2290	GT	GGG
(GAG)	 AG	2311-2324	GT	AGG
add_exon() Sorry, GeneMark_model.109044_t 1899-1952-terminal-1 is invalid.
-recovered GeneMark_model.109044_t, terminal, 1899, 1952
-recovered GeneMark_model.109044_t, internal, 435, 619
-recovered GeneMark_model.109044_t, internal, 1815, 1830
-recovered GeneMark_model.109044_t, internal, 1854, 1868
-recovered GeneMark_model.109044_t, internal, 1899, 1952
-recovered GeneMark_model.109044_t, internal, 1981, 1986
-recovered GeneMark_model.109044_t, internal, 2015, 2029
-recovered GeneMark_model.109044_t, internal, 2055, 2072
-recovered GeneMark_model.109044_t, internal, 2097, 2204
-recovered GeneMark_model.109044_t, internal, 2226, 2255
-recovered GeneMark_model.109044_t, internal, 2276, 2290
-recovered GeneMark_model.109044_t, internal, 2311, 2324

-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 - 2955
-exon list size: 32


building trellis

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29.4    
32.4    
35.3    
38.2    
41.2    
44.1    
47.1    
50.0    
52.9    
55.9    
58.8    
61.8    
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67.6    
70.6    
73.5    
76.5    
79.4    
82.4    
85.3    
88.2    
91.2    
94.1    
97.1    
-found 1 predictions from path traversal

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