-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1108

-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_62470-T1
Couldn't classify 2811, 2980
Sorry, prediction snap_scaffold_1108-snap.1-T1 fails validation.
(ATG)	 AG	652-780	GT	AGG
(GAG)	 AG	1408-2083	GT	AGG
(GTC)	 AG	2432-2612	GT	AGG
(CTG)	 AG	2811-2980	GT	GAG
add_exon() Sorry, snap_scaffold_1108-snap.1-T1 652-780-initial-1 is invalid.
-recovered snap_scaffold_1108-snap.1-T1, initial, 652, 780
-recovered snap_scaffold_1108-snap.1-T1, internal, 652, 780
-recovered snap_scaffold_1108-snap.1-T1, internal, 1408, 2083
-recovered snap_scaffold_1108-snap.1-T1, internal, 2432, 2612
-recovered snap_scaffold_1108-snap.1-T1, internal, 2811, 2980
Valid prediction for Augustus_model.g41531.t1
add_exon() Sorry, Augustus_model.g41531.t1 652-780-initial-1 is invalid.
add_exon() Sorry, Augustus_model.g41531.t1 1408-2083-internal-1 is invalid.
add_exon() Sorry, Augustus_model.g41531.t1 2432-2612-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g41531.t1 2811-2984-terminal-3 is invalid.
Couldn't classify 1854, 2083
Couldn't classify 2432, 2555
Sorry, prediction pasa_asmbl_7363.p1 fails validation.
(AGC)	 CC	1854-2083	GT	AGG
(GTC)	 AG	2432-2555	GC	AGG
-recovered pasa_asmbl_7363.p1, internal, 2432, 2555
Couldn't classify 3211, 3235
Sorry, prediction GeneMark_model.108904_t fails validation.
(ATG)	 AG	652-780	GT	AGG
(GAG)	 AG	1408-2083	GT	AGG
(GTC)	 AG	2432-2612	GT	AGG
(CTG)	 AG	2811-2980	GT	GAG
(TGA)	 AG	3012-3074	GT	ATG
(TGA)	 AG	3098-3127	GT	GAG
(GAG)	 AG	3149-3178	GT	GAG
(TGA)	 AG	3211-3235	GT	GAG
add_exon() Sorry, GeneMark_model.108904_t 652-780-initial-1 is invalid.
-recovered GeneMark_model.108904_t, initial, 652, 780
-recovered GeneMark_model.108904_t, internal, 652, 780
-recovered GeneMark_model.108904_t, internal, 1408, 2083
-recovered GeneMark_model.108904_t, internal, 2432, 2612
-recovered GeneMark_model.108904_t, internal, 2811, 2980
-recovered GeneMark_model.108904_t, internal, 3012, 3074
-recovered GeneMark_model.108904_t, internal, 3098, 3127
-recovered GeneMark_model.108904_t, internal, 3149, 3178
-recovered GeneMark_model.108904_t, internal, 3211, 3235

-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 - 3269
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-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