-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_193

-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 snap_scaffold_193-snap.1-T1
Valid prediction for HiQ_model.g40885.t1
Couldn't classify 9911, 9938
Sorry, prediction GeneMark_model.106891_t fails validation.
(ATG)	 CC	2527-2695	GT	TGG
(CCC)	 AG	3287-3299	GT	AGG
(AGA)	 AG	3329-3345	GT	TAG
(GAG)	 AG	3478-3565	GT	AAG
(ACG)	 AG	5117-5192	GT	ACG
(AGA)	 AG	5266-5390	GT	CGG
(TAA)	 AG	5595-5603	GT	GTG
(ACA)	 AG	5633-5674	GT	GGG
(GGA)	 AG	5704-5817	GT	AAG
(AGG)	 AG	6507-6512	GT	GAG
(GGA)	 AG	6540-6590	GT	AGG
(GGA)	 AG	6617-6637	GT	GGG
(GGA)	 AG	6669-6680	GT	AGG
(ACC)	 AG	6778-6857	GT	AGG
(CCA)	 AG	7834-7989	GT	AGG
(GCA)	 AG	9911-9938	GC	AAG
-recovered GeneMark_model.106891_t, initial, 2527, 2695
-recovered GeneMark_model.106891_t, internal, 3287, 3299
-recovered GeneMark_model.106891_t, internal, 3329, 3345
-recovered GeneMark_model.106891_t, internal, 3478, 3565
-recovered GeneMark_model.106891_t, internal, 5117, 5192
-recovered GeneMark_model.106891_t, internal, 5266, 5390
-recovered GeneMark_model.106891_t, internal, 5595, 5603
-recovered GeneMark_model.106891_t, internal, 5633, 5674
-recovered GeneMark_model.106891_t, internal, 5704, 5817
-recovered GeneMark_model.106891_t, internal, 6507, 6512
-recovered GeneMark_model.106891_t, internal, 6540, 6590
-recovered GeneMark_model.106891_t, internal, 6617, 6637
-recovered GeneMark_model.106891_t, internal, 6669, 6680
-recovered GeneMark_model.106891_t, internal, 6778, 6857
-recovered GeneMark_model.106891_t, internal, 7834, 7989
-recovered GeneMark_model.106891_t, internal, 9911, 9938
Valid prediction for GlimmerHMM_glimmerT_61480-T1
Valid prediction for Augustus_model.g40886.t1
Valid prediction for snap_scaffold_193-snap.2-T1
Couldn't classify 2256, 2394
Couldn't classify 3438, 3566
Sorry, prediction pasa_asmbl_22783.p1 fails validation.
(ATA)	 CA	2256-2394	GT	CTG
(GCA)	 AG	2501-2695	GT	TGG
(ATG)	 AG	3154-3299	GT	AGG
(GAA)	 AG	3438-3566	TA	AGT
add_exon() Sorry, pasa_asmbl_22783.p1 3154-3299-initial-1 is invalid.
-recovered pasa_asmbl_22783.p1, initial, 3154, 3299
-recovered pasa_asmbl_22783.p1, internal, 2501, 2695
-recovered pasa_asmbl_22783.p1, internal, 3154, 3299
Valid prediction for GlimmerHMM_glimmerT_61479-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 - 9957
-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 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support