-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_304

-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_61665-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: -)Valid prediction for GlimmerHMM_glimmerT_61664-T1
Couldn't classify 505, 513
Couldn't classify 7155, 7275
Sorry, prediction GeneMark_model.107242_t fails validation.
(GGG)	 AG	505-513	GT	AGG
(GGT)	 AG	535-565	GT	AAG
(CAC)	 AG	2118-2318	GT	AGG
(TCC)	 AG	2854-2990	GT	CTG
(TTA)	 AG	3453-3686	GT	CTG
(TCT)	 AG	3875-3899	GT	CTG
(GAA)	 AG	3927-4006	GT	GGG
(CTA)	 AG	4068-4163	GT	GAG
(GAG)	 AG	4659-4673	GT	GAG
(GGG)	 AG	4697-4740	GT	TGG
(AGA)	 AG	4792-4822	GT	GGG
(TGA)	 AG	4847-4906	GT	GAG
(ACA)	 AG	4947-5006	GT	GGG
(GAA)	 AG	5054-5061	GT	AGG
(GGC)	 AG	5215-5302	GT	ATG
(ATC)	 AG	5327-5498	GT	GGG
(TTC)	 AG	6195-6349	GT	GGG
(GCA)	 AG	6381-6429	GT	CCG
(GAT)	 AG	7121-7131	GT	ACG
(GAG)	 AG	7155-7275	GT	AGG
-recovered GeneMark_model.107242_t, terminal, 4659, 4673
-recovered GeneMark_model.107242_t, internal, 505, 513
-recovered GeneMark_model.107242_t, internal, 535, 565
-recovered GeneMark_model.107242_t, internal, 2118, 2318
-recovered GeneMark_model.107242_t, internal, 2854, 2990
-recovered GeneMark_model.107242_t, internal, 3453, 3686
-recovered GeneMark_model.107242_t, internal, 3875, 3899
-recovered GeneMark_model.107242_t, internal, 3927, 4006
-recovered GeneMark_model.107242_t, internal, 4068, 4163
-recovered GeneMark_model.107242_t, internal, 4659, 4673
-recovered GeneMark_model.107242_t, internal, 4697, 4740
-recovered GeneMark_model.107242_t, internal, 4792, 4822
-recovered GeneMark_model.107242_t, internal, 4847, 4906
-recovered GeneMark_model.107242_t, internal, 4947, 5006
-recovered GeneMark_model.107242_t, internal, 5054, 5061
-recovered GeneMark_model.107242_t, internal, 5215, 5302
-recovered GeneMark_model.107242_t, internal, 5327, 5498
-recovered GeneMark_model.107242_t, internal, 6195, 6349
-recovered GeneMark_model.107242_t, internal, 6381, 6429
-recovered GeneMark_model.107242_t, internal, 7121, 7131
-recovered GeneMark_model.107242_t, internal, 7155, 7275
Couldn't classify 7121, 7275
Sorry, prediction Augustus_model.g40998.t1 fails validation.
(ATG)	 AG	2172-2318	GT	AGG
(TCC)	 AG	2854-3008	GT	TAG
(TTA)	 AG	3453-3581	GT	AGG
(CTA)	 AG	4068-4196	GT	AGG
(AGG)	 AG	4362-4456	GT	ATG
(GAT)	 AG	7121-7275	GT	AGG
-recovered Augustus_model.g40998.t1, initial, 2172, 2318
-recovered Augustus_model.g40998.t1, internal, 2172, 2318
-recovered Augustus_model.g40998.t1, internal, 2854, 3008
-recovered Augustus_model.g40998.t1, internal, 3453, 3581
-recovered Augustus_model.g40998.t1, internal, 4068, 4196
-recovered Augustus_model.g40998.t1, internal, 4362, 4456
-recovered Augustus_model.g40998.t1, internal, 7121, 7275
Couldn't classify 2118, 2318
Couldn't classify 7121, 7275
Sorry, prediction snap_scaffold_304-snap.1-T1 fails validation.
(CAC)	 AG	2118-2318	GT	AGG
(TCC)	 AG	2854-3008	GT	TAG
(TTA)	 AG	3453-3686	GT	CTG
(CTA)	 AG	4068-4196	GT	AGG
(AGA)	 AG	4792-4822	GT	GGG
(CTT)	 AG	5079-5520	GT	GAG
(GAT)	 AG	7121-7275	GT	AGG
-recovered snap_scaffold_304-snap.1-T1, internal, 2118, 2318
-recovered snap_scaffold_304-snap.1-T1, internal, 2854, 3008
-recovered snap_scaffold_304-snap.1-T1, internal, 3453, 3686
-recovered snap_scaffold_304-snap.1-T1, internal, 4068, 4196
-recovered snap_scaffold_304-snap.1-T1, internal, 4792, 4822
-recovered snap_scaffold_304-snap.1-T1, internal, 5079, 5520
-recovered snap_scaffold_304-snap.1-T1, internal, 7121, 7275
Couldn't classify 2160, 2318
Couldn't classify 2854, 3003
Sorry, prediction pasa_asmbl_40867.p1 fails validation.
(TTC)	 CC	2160-2318	GT	AGG
(TCC)	 AG	2854-3003	AA	CCA
Couldn't classify 2118, 2318
Sorry, prediction GlimmerHMM_glimmerT_61666-T1 fails validation.
(CAC)	 AG	2118-2318	GT	AGG
(TCC)	 AG	2854-3009	TA	AGT
-recovered GlimmerHMM_glimmerT_61666-T1, terminal, 2854, 3009
-recovered GlimmerHMM_glimmerT_61666-T1, internal, 2118, 2318

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

-building trellis in range 1 - 8391
-exon list size: 60


building trellis

1.6    
3.2    
4.8    
6.5    
8.1    
9.7    
11.3    
12.9    
14.5    
16.1    
17.7    
19.4    
21.0    
22.6    
24.2    
25.8    
27.4    
29.0    
30.6    
32.3    
33.9    
35.5    
37.1    
38.7    
40.3    
41.9    
43.5    
45.2    
46.8    
48.4    
50.0    
51.6    
53.2    
54.8    
56.5    
58.1    
59.7    
61.3    
62.9    
64.5    
66.1    
67.7    
69.4    
71.0    
72.6    
74.2    
75.8    
77.4    
79.0    
80.6    
82.3    
83.9    
85.5    
87.1    
88.7    
90.3    
91.9    
93.5    
95.2    
96.8    
98.4    
-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