-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_947

-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: +)Couldn't classify 434, 708
Couldn't classify 3722, 3730
Sorry, prediction Augustus_model.g41453.t1 fails validation.
(ACT)	 AG	434-708	GT	CTG
(GTA)	 AG	954-1007	GT	AGG
(GTT)	 AG	1375-1452	GT	AGG
(GCC)	 AG	1552-1917	GT	AGG
(AGC)	 AG	2176-2280	GT	AGG
(GGA)	 AG	2368-2547	GT	AGG
(GCA)	 AG	2633-2731	GT	AGG
(AGT)	 AG	3073-3589	GT	AGG
(CAA)	 AG	3722-3730	GT	GGG
-recovered Augustus_model.g41453.t1, internal, 434, 708
-recovered Augustus_model.g41453.t1, internal, 954, 1007
-recovered Augustus_model.g41453.t1, internal, 1375, 1452
-recovered Augustus_model.g41453.t1, internal, 1552, 1917
-recovered Augustus_model.g41453.t1, internal, 2176, 2280
-recovered Augustus_model.g41453.t1, internal, 2368, 2547
-recovered Augustus_model.g41453.t1, internal, 2633, 2731
-recovered Augustus_model.g41453.t1, internal, 3073, 3589
-recovered Augustus_model.g41453.t1, internal, 3722, 3730
Valid prediction for GlimmerHMM_glimmerT_62355-T1
add_exon() Sorry, GlimmerHMM_glimmerT_62355-T1 434-837-terminal-1 is invalid.
Couldn't classify 434, 708
Couldn't classify 3722, 3834
Sorry, prediction snap_scaffold_947-snap.1-T1 fails validation.
(ACT)	 AG	434-708	GT	CTG
(GTA)	 AG	954-1007	GT	AGG
(GCC)	 AG	1552-1917	GT	AGG
(AGC)	 AG	2176-2280	GT	AGG
(GGA)	 AG	2368-2547	GT	AGG
(GCA)	 AG	2633-2731	GT	AGG
(AGT)	 AG	3073-3589	GT	AGG
(CAA)	 AG	3722-3834	GT	AGG
-recovered snap_scaffold_947-snap.1-T1, internal, 434, 708
-recovered snap_scaffold_947-snap.1-T1, internal, 954, 1007
-recovered snap_scaffold_947-snap.1-T1, internal, 1552, 1917
-recovered snap_scaffold_947-snap.1-T1, internal, 2176, 2280
-recovered snap_scaffold_947-snap.1-T1, internal, 2368, 2547
-recovered snap_scaffold_947-snap.1-T1, internal, 2633, 2731
-recovered snap_scaffold_947-snap.1-T1, internal, 3073, 3589
-recovered snap_scaffold_947-snap.1-T1, internal, 3722, 3834
Couldn't classify 3722, 3834
Sorry, prediction pasa_asmbl_55810.p1 fails validation.
(ATG)	 TG	1726-1917	GT	AGG
(AGC)	 AG	2176-2280	GT	AGG
(GGA)	 AG	2368-2547	GT	AGG
(GCA)	 AG	2633-2731	GT	AGG
(AGT)	 AG	3073-3589	GT	AGG
(CAA)	 AG	3722-3834	GT	AGG
-recovered pasa_asmbl_55810.p1, initial, 1726, 1917
-recovered pasa_asmbl_55810.p1, internal, 2176, 2280
-recovered pasa_asmbl_55810.p1, internal, 2368, 2547
-recovered pasa_asmbl_55810.p1, internal, 2633, 2731
-recovered pasa_asmbl_55810.p1, internal, 3073, 3589
-recovered pasa_asmbl_55810.p1, internal, 3722, 3834
Couldn't classify 3719, 3834
Sorry, prediction GeneMark_model.108647_t fails validation.
(ATG)	 GC	1739-1749	GT	GGG
(AGA)	 AG	1776-1917	GT	AGG
(AGC)	 AG	2176-2280	GT	AGG
(GGA)	 AG	2368-2547	GT	AGG
(GCA)	 AG	2633-2731	GT	AGG
(AGT)	 AG	3073-3589	GT	AGG
(CAG)	 AG	3719-3834	GT	AGG
-recovered GeneMark_model.108647_t, initial, 1739, 1749
-recovered GeneMark_model.108647_t, internal, 1776, 1917
-recovered GeneMark_model.108647_t, internal, 2176, 2280
-recovered GeneMark_model.108647_t, internal, 2368, 2547
-recovered GeneMark_model.108647_t, internal, 2633, 2731
-recovered GeneMark_model.108647_t, internal, 3073, 3589
-recovered GeneMark_model.108647_t, internal, 3719, 3834
Couldn't classify 3073, 3589
Sorry, prediction GlimmerHMM_glimmerT_62356-T1 fails validation.
(ATG)	 CC	1423-1452	GT	AGG
(GCC)	 AG	1552-1815	GT	CTG
(AGC)	 AG	2176-2280	GT	AGG
(GGA)	 AG	2368-2547	GT	AGG
(GCA)	 AG	2633-2731	GT	AGG
(AGT)	 AG	3073-3589	GT	AGG
-recovered GlimmerHMM_glimmerT_62356-T1, initial, 1423, 1452
-recovered GlimmerHMM_glimmerT_62356-T1, internal, 1552, 1815
-recovered GlimmerHMM_glimmerT_62356-T1, internal, 2176, 2280
-recovered GlimmerHMM_glimmerT_62356-T1, internal, 2368, 2547
-recovered GlimmerHMM_glimmerT_62356-T1, internal, 2633, 2731
-recovered GlimmerHMM_glimmerT_62356-T1, internal, 3073, 3589

-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 3716, 3722
Sorry, prediction GeneMark_model.108646_t fails validation.
(ATG)	 GC	2172-2236	GT	GAG
(AAG)	 AG	2580-2675	GC	AGG
(AGG)	 AG	2699-2707	GT	AGG
(GAA)	 AG	2742-2771	GT	ATG
(GCA)	 AG	2795-2935	GT	GTG
(AGA)	 AG	3439-3447	GT	AAG
(AAA)	 AG	3470-3517	GT	AAG
(GAT)	 AG	3540-3584	GT	AAG
(GAT)	 AG	3605-3611	GT	AGG
(GGG)	 AG	3628-3638	GT	AAG
(GAG)	 AG	3669-3695	GT	AAG
(GAT)	 AG	3716-3722	GT	AGG
-recovered GeneMark_model.108646_t, initial, 2172, 2236
-recovered GeneMark_model.108646_t, terminal, 2699, 2707
add_exon() Sorry, GeneMark_model.108646_t 3470-3517-terminal-1 is invalid.
-recovered GeneMark_model.108646_t, terminal, 3470, 3517
-recovered GeneMark_model.108646_t, internal, 2580, 2675
-recovered GeneMark_model.108646_t, internal, 2699, 2707
-recovered GeneMark_model.108646_t, internal, 2742, 2771
-recovered GeneMark_model.108646_t, internal, 2795, 2935
-recovered GeneMark_model.108646_t, internal, 3439, 3447
-recovered GeneMark_model.108646_t, internal, 3470, 3517
-recovered GeneMark_model.108646_t, internal, 3540, 3584
-recovered GeneMark_model.108646_t, internal, 3605, 3611
-recovered GeneMark_model.108646_t, internal, 3628, 3638
-recovered GeneMark_model.108646_t, internal, 3669, 3695
-recovered GeneMark_model.108646_t, internal, 3716, 3722

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

-building trellis in range 1 - 3865
-exon list size: 51


building trellis

1.9    
3.8    
5.7    
7.5    
9.4    
11.3    
13.2    
15.1    
17.0    
18.9    
20.8    
22.6    
24.5    
26.4    
28.3    
30.2    
32.1    
34.0    
35.8    
37.7    
39.6    
41.5    
43.4    
45.3    
47.2    
49.1    
50.9    
52.8    
54.7    
56.6    
58.5    
60.4    
62.3    
64.2    
66.0    
67.9    
69.8    
71.7    
73.6    
75.5    
77.4    
79.2    
81.1    
83.0    
84.9    
86.8    
88.7    
90.6    
92.5    
94.3    
96.2    
98.1    
-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