-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/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

-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 411, 541
Sorry, prediction Augustus_model.g40146.t1 fails validation.
(AGC)	 AG	411-541	GT	AGG
(GTT)	 AG	808-979	GT	AGG
(ACT)	 AG	1382-1491	CC	GAC
-recovered Augustus_model.g40146.t1, terminal, 1382, 1491
-recovered Augustus_model.g40146.t1, internal, 411, 541
-recovered Augustus_model.g40146.t1, internal, 808, 979
Couldn't classify 411, 541
Sorry, prediction GlimmerHMM_glimmerT_60652-T1 fails validation.
(AGC)	 AG	411-541	GT	AGG
(GTT)	 AG	808-979	GT	AGG
(ACT)	 AG	1382-1491	CC	GAC
-recovered GlimmerHMM_glimmerT_60652-T1, terminal, 1382, 1491
-recovered GlimmerHMM_glimmerT_60652-T1, internal, 411, 541
-recovered GlimmerHMM_glimmerT_60652-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 4710, 4795
Sorry, prediction Augustus_model.g40145.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.g40145.t1, initial, 2659, 2802
add_exon() Sorry, Augustus_model.g40145.t1 2926-3076-terminal-3 is invalid.
-recovered Augustus_model.g40145.t1, terminal, 2926, 3076
-recovered Augustus_model.g40145.t1, internal, 2926, 3076
-recovered Augustus_model.g40145.t1, internal, 3350, 3454
-recovered Augustus_model.g40145.t1, internal, 3567, 3817
-recovered Augustus_model.g40145.t1, internal, 4118, 4292
-recovered Augustus_model.g40145.t1, internal, 4710, 4795
Valid prediction for GlimmerHMM_glimmerT_60651-T1
Couldn't classify 2668, 2802
Couldn't classify 4710, 4750
Sorry, prediction pasa_asmbl_51610.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_51610.p1 2926-3076-terminal-3 is invalid.
-recovered pasa_asmbl_51610.p1, terminal, 2926, 3076
-recovered pasa_asmbl_51610.p1, internal, 2926, 3076
-recovered pasa_asmbl_51610.p1, internal, 3350, 3454
-recovered pasa_asmbl_51610.p1, internal, 3567, 3817
-recovered pasa_asmbl_51610.p1, internal, 4118, 4292

-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: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-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