-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_148

-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: +)
-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 12410, 12574
Sorry, prediction snap_scaffold_148-snap.1-T1 fails validation.
(ATG)	 GA	10985-11201	GT	AGG
(ATT)	 AG	11481-12070	GT	GGG
(TCT)	 AG	12100-12393	GT	GGG
(TTT)	 AG	12410-12574	GT	CGG
-recovered snap_scaffold_148-snap.1-T1, initial, 10985, 11201
-recovered snap_scaffold_148-snap.1-T1, internal, 11481, 12070
-recovered snap_scaffold_148-snap.1-T1, internal, 12100, 12393
-recovered snap_scaffold_148-snap.1-T1, internal, 12410, 12574
Couldn't classify 55, 167
Sorry, prediction GeneMark_model.106741_t fails validation.
(GTA)	 AG	55-167	GT	AAG
(ATG)	 AG	190-206	GT	CGG
(AGG)	 AG	231-296	GT	AGG
(GAG)	 AG	324-344	GT	GAG
(GAG)	 AG	432-514	GT	GGG
(GTA)	 AG	755-910	GT	AGG
(GAG)	 AG	1167-1333	GT	AGG
(GAG)	 AG	1826-1839	GT	GAG
(GAG)	 AG	3128-3198	GT	AGG
(ACC)	 AG	3684-3877	GT	AGG
(GTT)	 AG	4947-5081	GT	TTG
(GAT)	 AG	6761-6859	TG	AGT
-recovered GeneMark_model.106741_t, initial, 190, 206
-recovered GeneMark_model.106741_t, terminal, 6761, 6859
-recovered GeneMark_model.106741_t, internal, 55, 167
-recovered GeneMark_model.106741_t, internal, 190, 206
-recovered GeneMark_model.106741_t, internal, 231, 296
-recovered GeneMark_model.106741_t, internal, 324, 344
-recovered GeneMark_model.106741_t, internal, 432, 514
-recovered GeneMark_model.106741_t, internal, 755, 910
-recovered GeneMark_model.106741_t, internal, 1167, 1333
-recovered GeneMark_model.106741_t, internal, 1826, 1839
-recovered GeneMark_model.106741_t, internal, 3128, 3198
-recovered GeneMark_model.106741_t, internal, 3684, 3877
-recovered GeneMark_model.106741_t, internal, 4947, 5081
Couldn't classify 55, 206
Sorry, prediction snap_scaffold_148-snap.6-T1 fails validation.
(GTA)	 AG	55-206	GT	CGG
(GTC)	 AG	418-514	GT	GGG
(GTA)	 AG	755-910	GT	AGG
(GAG)	 AG	1167-1333	GT	AGG
(GGA)	 AG	1720-1818	GG	GAG
-recovered snap_scaffold_148-snap.6-T1, terminal, 1720, 1818
-recovered snap_scaffold_148-snap.6-T1, internal, 55, 206
-recovered snap_scaffold_148-snap.6-T1, internal, 418, 514
-recovered snap_scaffold_148-snap.6-T1, internal, 755, 910
-recovered snap_scaffold_148-snap.6-T1, internal, 1167, 1333
Valid prediction for GlimmerHMM_glimmerT_61393-T1
Valid prediction for Augustus_model.g40833.t1
Valid prediction for snap_scaffold_148-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_61394-T1
Couldn't classify 54, 206
Sorry, prediction pasa_asmbl_13880.p1 fails validation.
(GGT)	 CA	54-206	GT	CGG
(GTC)	 AG	418-514	GT	GGG
(GTA)	 AG	755-910	GT	AGG
(GAG)	 AG	1167-1333	GT	AGG
(GGA)	 AG	1720-1818	GG	GAG
-recovered pasa_asmbl_13880.p1, terminal, 1720, 1818
-recovered pasa_asmbl_13880.p1, internal, 418, 514
-recovered pasa_asmbl_13880.p1, internal, 755, 910
-recovered pasa_asmbl_13880.p1, internal, 1167, 1333
Couldn't classify 9444, 9489
Sorry, prediction pasa_asmbl_13879.p1 fails validation.
(ATG)	 AG	6251-6315	GT	AGG
(GAA)	 AG	6517-6610	GT	AGG
(GAT)	 AG	6761-6858	GT	TAG
(CTG)	 AG	7214-7354	GT	AGG
(GTA)	 AG	7709-7824	GT	GGG
(GTT)	 AG	8614-8672	GT	AGG
(CTG)	 AG	9011-9162	GT	AAG
(AGA)	 AG	9444-9489	GA	CGG
-recovered pasa_asmbl_13879.p1, initial, 6251, 6315
-recovered pasa_asmbl_13879.p1, internal, 6251, 6315
-recovered pasa_asmbl_13879.p1, internal, 6517, 6610
-recovered pasa_asmbl_13879.p1, internal, 6761, 6858
-recovered pasa_asmbl_13879.p1, internal, 7214, 7354
-recovered pasa_asmbl_13879.p1, internal, 7709, 7824
-recovered pasa_asmbl_13879.p1, internal, 8614, 8672
-recovered pasa_asmbl_13879.p1, internal, 9011, 9162
Valid prediction for snap_scaffold_148-snap.4-T1
Couldn't classify 12403, 12579
Sorry, prediction GeneMark_model.106739_t fails validation.
(ATG)	 GA	10985-11201	GT	AGG
(ATT)	 AG	11481-12070	GT	GGG
(TCT)	 AG	12100-12338	GT	CAG
(GGT)	 AG	12403-12579	GT	CTG
-recovered GeneMark_model.106739_t, initial, 10985, 11201
-recovered GeneMark_model.106739_t, internal, 11481, 12070
-recovered GeneMark_model.106739_t, internal, 12100, 12338
-recovered GeneMark_model.106739_t, internal, 12403, 12579
Valid prediction for snap_scaffold_148-snap.5-T1
Valid prediction for HiQ_model.g40832.t1
Valid prediction for GlimmerHMM_glimmerT_61391-T1
Couldn't classify 80, 206
Sorry, prediction Augustus_model.g40834.t1 fails validation.
(CGA)	 AG	80-206	GT	CGG
(GTC)	 AG	418-514	GT	GGG
(GTA)	 AG	755-910	GT	AGG
(GAG)	 AG	1167-1333	GT	AGG
(GGA)	 AG	1720-1818	GG	GAG
-recovered Augustus_model.g40834.t1, terminal, 1720, 1818
-recovered Augustus_model.g40834.t1, internal, 80, 206
-recovered Augustus_model.g40834.t1, internal, 418, 514
-recovered Augustus_model.g40834.t1, internal, 755, 910
-recovered Augustus_model.g40834.t1, internal, 1167, 1333
Valid prediction for GlimmerHMM_glimmerT_61395-T1
Valid prediction for GeneMark_model.106740_t
Couldn't classify 12314, 12588
Sorry, prediction Augustus_model.g40831.t1 fails validation.
(ATG)	 GA	10985-11201	GT	AGG
(ATT)	 AG	11481-12115	GT	GGG
(TCG)	 AG	12314-12588		GT
-recovered Augustus_model.g40831.t1, initial, 10985, 11201
-recovered Augustus_model.g40831.t1, internal, 11481, 12115
Couldn't classify 93, 206
Sorry, prediction GlimmerHMM_glimmerT_61396-T1 fails validation.
(GAG)	 AG	93-206	GT	CGG
(GTC)	 AG	418-514	GT	GGG
(GTA)	 AG	755-910	GT	AGG
(GAG)	 AG	1167-1333	GT	AGG
(GGA)	 AG	1720-1818	GG	GAG
-recovered GlimmerHMM_glimmerT_61396-T1, terminal, 1720, 1818
-recovered GlimmerHMM_glimmerT_61396-T1, internal, 93, 206
-recovered GlimmerHMM_glimmerT_61396-T1, internal, 418, 514
-recovered GlimmerHMM_glimmerT_61396-T1, internal, 755, 910
-recovered GlimmerHMM_glimmerT_61396-T1, internal, 1167, 1333
Valid prediction for GlimmerHMM_glimmerT_61392-T1
Valid prediction for snap_scaffold_148-snap.3-T1

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

-building trellis in range 1 - 12588
-exon list size: 79


building trellis

1.2    
2.5    
3.7    
4.9    
6.2    
7.4    
8.6    
9.9    
11.1    
12.3    
13.6    
14.8    
16.0    
17.3    
18.5    
19.8    
21.0    
22.2    
23.5    
24.7    
25.9    
27.2    
28.4    
29.6    
30.9    
32.1    
33.3    
34.6    
35.8    
37.0    
38.3    
39.5    
40.7    
42.0    
43.2    
44.4    
45.7    
46.9    
48.1    
49.4    
50.6    
51.9    
53.1    
54.3    
55.6    
56.8    
58.0    
59.3    
60.5    
61.7    
63.0    
64.2    
65.4    
66.7    
67.9    
69.1    
70.4    
71.6    
72.8    
74.1    
75.3    
76.5    
77.8    
79.0    
80.2    
81.5    
82.7    
84.0    
85.2    
86.4    
87.7    
88.9    
90.1    
91.4    
92.6    
93.8    
95.1    
96.3    
97.5    
98.8    
-found 5 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 5 predictions persist after filtering for low support