-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_716

-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 3996, 4138
Sorry, prediction snap_scaffold_716-snap.2-T1 fails validation.
(ATG)	 GG	3068-3259	GT	AGG
(GGG)	 AG	3359-3410	GT	TGG
(GAC)	 AG	3996-4138	GT	AGG
-recovered snap_scaffold_716-snap.2-T1, initial, 3068, 3259
-recovered snap_scaffold_716-snap.2-T1, internal, 3359, 3410
-recovered snap_scaffold_716-snap.2-T1, internal, 3996, 4138
Valid prediction for GeneMark_model.108248_t

-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 2668, 2802
Couldn't classify 4710, 4750
Sorry, prediction pasa_asmbl_51560.p1 fails validation.
(GTG)	 TG	2668-2802	GT	AGG
(TAC)	 AG	2926-3076	GT	GAG
(GTG)	 AG	3350-3454	GT	AGG
(ACT)	 AG	3567-3817	GT	AGG
(ACA)	 AG	4118-4292	GT	GGG
(GGG)	 AG	4710-4750	CC	ACC
add_exon() Sorry, pasa_asmbl_51560.p1 2926-3076-terminal-3 is invalid.
-recovered pasa_asmbl_51560.p1, terminal, 2926, 3076
-recovered pasa_asmbl_51560.p1, internal, 2926, 3076
-recovered pasa_asmbl_51560.p1, internal, 3350, 3454
-recovered pasa_asmbl_51560.p1, internal, 3567, 3817
-recovered pasa_asmbl_51560.p1, internal, 4118, 4292
Couldn't classify 4710, 4795
Sorry, prediction Augustus_model.g41311.t1 fails validation.
(ATG)	 CA	2659-2802	GT	AGG
(TAC)	 AG	2926-3076	GT	GAG
(GTG)	 AG	3350-3454	GT	AGG
(ACT)	 AG	3567-3817	GT	AGG
(ACA)	 AG	4118-4292	GT	GGG
(GGG)	 AG	4710-4795	GT	AGG
-recovered Augustus_model.g41311.t1, initial, 2659, 2802
add_exon() Sorry, Augustus_model.g41311.t1 2926-3076-terminal-3 is invalid.
-recovered Augustus_model.g41311.t1, terminal, 2926, 3076
-recovered Augustus_model.g41311.t1, internal, 2926, 3076
-recovered Augustus_model.g41311.t1, internal, 3350, 3454
-recovered Augustus_model.g41311.t1, internal, 3567, 3817
-recovered Augustus_model.g41311.t1, internal, 4118, 4292
-recovered Augustus_model.g41311.t1, internal, 4710, 4795
Valid prediction for GlimmerHMM_glimmerT_62152-T1
Couldn't classify 411, 541
Sorry, prediction Augustus_model.g41312.t1 fails validation.
(AGC)	 AG	411-541	GT	AGG
(GTT)	 AG	808-979	GT	AGG
(ACT)	 AG	1382-1491	CC	GAC
-recovered Augustus_model.g41312.t1, terminal, 1382, 1491
-recovered Augustus_model.g41312.t1, internal, 411, 541
-recovered Augustus_model.g41312.t1, internal, 808, 979
Couldn't classify 411, 541
Sorry, prediction snap_scaffold_716-snap.1-T1 fails validation.
(AGC)	 AG	411-541	GT	AGG
(GTT)	 AG	808-979	GT	AGG
(ACT)	 AG	1382-1467	GT	ACG
(CTC)	 AG	2638-2802	GT	AGG
(TAC)	 AG	2926-3076	GT	GAG
(GTG)	 AG	3350-3454	GT	AGG
(ACT)	 AG	3567-3817	GT	AGG
(ACA)	 AG	4118-4330	CT	AGC
add_exon() Sorry, snap_scaffold_716-snap.1-T1 2926-3076-terminal-3 is invalid.
-recovered snap_scaffold_716-snap.1-T1, terminal, 2926, 3076
-recovered snap_scaffold_716-snap.1-T1, terminal, 4118, 4330
-recovered snap_scaffold_716-snap.1-T1, internal, 411, 541
-recovered snap_scaffold_716-snap.1-T1, internal, 808, 979
-recovered snap_scaffold_716-snap.1-T1, internal, 1382, 1467
-recovered snap_scaffold_716-snap.1-T1, internal, 2638, 2802
-recovered snap_scaffold_716-snap.1-T1, internal, 2926, 3076
-recovered snap_scaffold_716-snap.1-T1, internal, 3350, 3454
-recovered snap_scaffold_716-snap.1-T1, internal, 3567, 3817
Couldn't classify 411, 541
Sorry, prediction GlimmerHMM_glimmerT_62153-T1 fails validation.
(AGC)	 AG	411-541	GT	AGG
(GTT)	 AG	808-979	GT	AGG
(ACT)	 AG	1382-1491	CC	GAC
-recovered GlimmerHMM_glimmerT_62153-T1, terminal, 1382, 1491
-recovered GlimmerHMM_glimmerT_62153-T1, internal, 411, 541
-recovered GlimmerHMM_glimmerT_62153-T1, internal, 808, 979
Couldn't classify 4710, 4795
Sorry, prediction GeneMark_model.108247_t fails validation.
(ATG)	 CA	2659-2802	GT	AGG
(TAC)	 AG	2926-3076	GT	GAG
(GTG)	 AG	3350-3454	GT	AGG
(ACT)	 AG	3567-3909	GT	AGG
(AGA)	 AG	3938-3955	GT	GAG
(ACA)	 AG	3982-4078	GT	CCG
(ACA)	 AG	4118-4292	GT	GGG
(GGG)	 AG	4710-4795	GT	AGG
-recovered GeneMark_model.108247_t, initial, 2659, 2802
add_exon() Sorry, GeneMark_model.108247_t 2926-3076-terminal-3 is invalid.
-recovered GeneMark_model.108247_t, terminal, 2926, 3076
-recovered GeneMark_model.108247_t, internal, 2926, 3076
-recovered GeneMark_model.108247_t, internal, 3350, 3454
-recovered GeneMark_model.108247_t, internal, 3567, 3909
-recovered GeneMark_model.108247_t, internal, 3938, 3955
-recovered GeneMark_model.108247_t, internal, 3982, 4078
-recovered GeneMark_model.108247_t, internal, 4118, 4292
-recovered GeneMark_model.108247_t, internal, 4710, 4795

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4456, rend_intergenic: 3068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 4866
-exon list size: 41


building trellis

2.3    
4.7    
7.0    
9.3    
11.6    
14.0    
16.3    
18.6    
20.9    
23.3    
25.6    
27.9    
30.2    
32.6    
34.9    
37.2    
39.5    
41.9    
44.2    
46.5    
48.8    
51.2    
53.5    
55.8    
58.1    
60.5    
62.8    
65.1    
67.4    
69.8    
72.1    
74.4    
76.7    
79.1    
81.4    
83.7    
86.0    
88.4    
90.7    
93.0    
95.3    
97.7    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 4456, rend_intergenic: 3068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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