-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_189

-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 481, 657
Sorry, prediction snap_scaffold_189-snap.2-T1 fails validation.
(GTG)	 AG	481-657	GT	AGG
(CCA)	 AG	4092-4286	GG	GAG
-recovered snap_scaffold_189-snap.2-T1, terminal, 4092, 4286
-recovered snap_scaffold_189-snap.2-T1, internal, 481, 657
Couldn't classify 9860, 9946
Sorry, prediction GeneMark_model.106879_t fails validation.
(ATG)	 AG	9009-9088	GC	GAG
(CGA)	 AG	9112-9126	GC	GAG
(AGA)	 AG	9150-9158	GC	GAG
(AGC)	 AG	9190-9222	GC	GAG
(AGC)	 AG	9254-9283	GT	AGG
(TGT)	 AG	9483-9512	GT	GAG
(GGA)	 AG	9548-9574	GT	AAG
(AAA)	 AG	9600-9614	GT	CAG
(CCT)	 AG	9860-9946	GT	GAG
-recovered GeneMark_model.106879_t, initial, 9009, 9088
-recovered GeneMark_model.106879_t, internal, 9009, 9088
-recovered GeneMark_model.106879_t, internal, 9112, 9126
-recovered GeneMark_model.106879_t, internal, 9150, 9158
-recovered GeneMark_model.106879_t, internal, 9190, 9222
-recovered GeneMark_model.106879_t, internal, 9254, 9283
-recovered GeneMark_model.106879_t, internal, 9483, 9512
-recovered GeneMark_model.106879_t, internal, 9548, 9574
-recovered GeneMark_model.106879_t, internal, 9600, 9614
-recovered GeneMark_model.106879_t, internal, 9860, 9946

-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 9832, 9913
Sorry, prediction GeneMark_model.106878_t fails validation.
(ATG)	 TA	3271-3278	GT	GCG
(GTC)	 AG	4646-4709	GT	AGG
(GTG)	 AG	4983-5096	GT	AGG
(CTG)	 AG	5530-5631	GT	GGG
(ATG)	 AG	5719-5911	GT	CTG
(GGA)	 AG	6372-6470	GT	AGG
(GGG)	 AG	7094-7206	GT	CTG
(ACC)	 AG	8364-8472	GT	TGG
(AGA)	 AG	8960-9083	GT	GAG
(GGT)	 AG	9364-9529	GT	AGG
(GCA)	 AG	9832-9913	GT	AGG
-recovered GeneMark_model.106878_t, initial, 3271, 3278
-recovered GeneMark_model.106878_t, initial, 5719, 5911
add_exon() Sorry, GeneMark_model.106878_t 8960-9083-terminal-3 is invalid.
-recovered GeneMark_model.106878_t, terminal, 8960, 9083
-recovered GeneMark_model.106878_t, internal, 4646, 4709
-recovered GeneMark_model.106878_t, internal, 4983, 5096
-recovered GeneMark_model.106878_t, internal, 5530, 5631
-recovered GeneMark_model.106878_t, internal, 5719, 5911
-recovered GeneMark_model.106878_t, internal, 6372, 6470
-recovered GeneMark_model.106878_t, internal, 7094, 7206
-recovered GeneMark_model.106878_t, internal, 8364, 8472
-recovered GeneMark_model.106878_t, internal, 8960, 9083
-recovered GeneMark_model.106878_t, internal, 9364, 9529
-recovered GeneMark_model.106878_t, internal, 9832, 9913
Couldn't classify 9832, 9913
Sorry, prediction snap_scaffold_189-snap.1-T1 fails validation.
(ATG)	 GA	4496-4573	GT	GAG
(GTG)	 AG	4983-5096	GT	AGG
(CTG)	 AG	5530-5631	GT	GGG
(ATG)	 AG	5719-5911	GT	CTG
(GGG)	 AG	7094-7206	GT	CTG
(ACC)	 AG	8364-8472	GT	TGG
(AGA)	 AG	8960-9045	GT	AGG
(AGG)	 AG	9362-9529	GT	AGG
(GCA)	 AG	9832-9913	GT	AGG
-recovered snap_scaffold_189-snap.1-T1, initial, 4496, 4573
-recovered snap_scaffold_189-snap.1-T1, initial, 5719, 5911
-recovered snap_scaffold_189-snap.1-T1, internal, 4983, 5096
-recovered snap_scaffold_189-snap.1-T1, internal, 5530, 5631
-recovered snap_scaffold_189-snap.1-T1, internal, 5719, 5911
-recovered snap_scaffold_189-snap.1-T1, internal, 7094, 7206
-recovered snap_scaffold_189-snap.1-T1, internal, 8364, 8472
-recovered snap_scaffold_189-snap.1-T1, internal, 8960, 9045
-recovered snap_scaffold_189-snap.1-T1, internal, 9362, 9529
-recovered snap_scaffold_189-snap.1-T1, internal, 9832, 9913
Couldn't classify 4983, 5096
Sorry, prediction GlimmerHMM_glimmerT_61473-T1 fails validation.
(GTG)	 AG	4983-5096	GT	AGG
(CTG)	 AG	5530-5631	GT	GGG
(ATG)	 AG	5719-5911	GT	CTG
(GGA)	 AG	6372-6470	GT	AGG
(GGG)	 AG	7094-7206	GT	CTG
(ACC)	 AG	8364-8472	GT	TGG
(AGA)	 AG	8960-9045	GT	AGG
(AGG)	 AG	9362-9556	AA	GAA
-recovered GlimmerHMM_glimmerT_61473-T1, initial, 5719, 5911
-recovered GlimmerHMM_glimmerT_61473-T1, terminal, 9362, 9556
-recovered GlimmerHMM_glimmerT_61473-T1, internal, 4983, 5096
-recovered GlimmerHMM_glimmerT_61473-T1, internal, 5530, 5631
-recovered GlimmerHMM_glimmerT_61473-T1, internal, 5719, 5911
-recovered GlimmerHMM_glimmerT_61473-T1, internal, 6372, 6470
-recovered GlimmerHMM_glimmerT_61473-T1, internal, 7094, 7206
-recovered GlimmerHMM_glimmerT_61473-T1, internal, 8364, 8472
-recovered GlimmerHMM_glimmerT_61473-T1, internal, 8960, 9045
Couldn't classify 9757, 9913
Sorry, prediction Augustus_model.g40882.t1 fails validation.
(ATG)	 AA	1778-1816	GT	TGG
(ACT)	 AG	4566-4709	GT	AGG
(GTG)	 AG	4983-5096	GT	AGG
(CTG)	 AG	5530-5631	GT	GGG
(ATG)	 AG	5719-5911	GT	CTG
(GGA)	 AG	6372-6470	GT	AGG
(GGG)	 AG	7094-7206	GT	CTG
(ACC)	 AG	8364-8472	GT	TGG
(AGA)	 AG	8960-9045	GT	AGG
(AGG)	 AG	9362-9529	GT	AGG
(TGG)	 AG	9757-9913	GT	AGG
-recovered Augustus_model.g40882.t1, initial, 1778, 1816
-recovered Augustus_model.g40882.t1, initial, 5719, 5911
-recovered Augustus_model.g40882.t1, internal, 4566, 4709
-recovered Augustus_model.g40882.t1, internal, 4983, 5096
-recovered Augustus_model.g40882.t1, internal, 5530, 5631
-recovered Augustus_model.g40882.t1, internal, 5719, 5911
-recovered Augustus_model.g40882.t1, internal, 6372, 6470
-recovered Augustus_model.g40882.t1, internal, 7094, 7206
-recovered Augustus_model.g40882.t1, internal, 8364, 8472
-recovered Augustus_model.g40882.t1, internal, 8960, 9045
-recovered Augustus_model.g40882.t1, internal, 9362, 9529
-recovered Augustus_model.g40882.t1, internal, 9757, 9913

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5505, rend_intergenic: 481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 10000
-exon list size: 49


building trellis

2.0    
3.9    
5.9    
7.8    
9.8    
11.8    
13.7    
15.7    
17.6    
19.6    
21.6    
23.5    
25.5    
27.5    
29.4    
31.4    
33.3    
35.3    
37.3    
39.2    
41.2    
43.1    
45.1    
47.1    
49.0    
51.0    
52.9    
54.9    
56.9    
58.8    
60.8    
62.7    
64.7    
66.7    
68.6    
70.6    
72.5    
74.5    
76.5    
78.4    
80.4    
82.4    
84.3    
86.3    
88.2    
90.2    
92.2    
94.1    
96.1    
98.0    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 5505, rend_intergenic: 481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support