-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_382

-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 298, 485
Couldn't classify 7004, 7137
Sorry, prediction snap_scaffold_382-snap.1-T1 fails validation.
(GAT)	 AG	298-485	GT	AGG
(TGG)	 AG	1714-1837	GT	AGG
(AGG)	 AG	2177-2340	GT	AGG
(CTG)	 AG	2708-2809	GT	AGG
(ATC)	 AG	3391-3540	GT	AGG
(GTG)	 AG	3750-3900	GT	TGG
(GGA)	 AG	4104-4228	GT	AGG
(CTG)	 AG	4407-4503	GT	CAG
(GGA)	 AG	4653-4777	GT	AGG
(CTG)	 AG	4858-4970	GT	AGG
(GGT)	 AG	5719-5853	GT	CAG
(GAC)	 AG	6246-6376	GT	GGG
(GTG)	 AG	6740-6876	GT	AGG
(GTG)	 AG	7004-7137	GT	AGG
-recovered snap_scaffold_382-snap.1-T1, internal, 298, 485
-recovered snap_scaffold_382-snap.1-T1, internal, 1714, 1837
-recovered snap_scaffold_382-snap.1-T1, internal, 2177, 2340
-recovered snap_scaffold_382-snap.1-T1, internal, 2708, 2809
-recovered snap_scaffold_382-snap.1-T1, internal, 3391, 3540
-recovered snap_scaffold_382-snap.1-T1, internal, 3750, 3900
-recovered snap_scaffold_382-snap.1-T1, internal, 4104, 4228
-recovered snap_scaffold_382-snap.1-T1, internal, 4407, 4503
-recovered snap_scaffold_382-snap.1-T1, internal, 4653, 4777
-recovered snap_scaffold_382-snap.1-T1, internal, 4858, 4970
-recovered snap_scaffold_382-snap.1-T1, internal, 5719, 5853
-recovered snap_scaffold_382-snap.1-T1, internal, 6246, 6376
-recovered snap_scaffold_382-snap.1-T1, internal, 6740, 6876
-recovered snap_scaffold_382-snap.1-T1, internal, 7004, 7137
Valid prediction for GlimmerHMM_glimmerT_61775-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61775-T1 298-512-terminal-1 is invalid.
Valid prediction for GeneMark_model.107480_t
add_exon() Sorry, GeneMark_model.107480_t 298-512-terminal-1 is invalid.
Couldn't classify 7004, 7137
Sorry, prediction GeneMark_model.107482_t fails validation.
(ATG)	 GG	1717-1837	GT	AGG
(AGG)	 AG	2177-2340	GT	AGG
(CTG)	 AG	2708-2809	GT	AGG
(ATC)	 AG	3391-3540	GT	AGG
(GTG)	 AG	3750-3900	GT	TGG
(GGA)	 AG	4104-4228	GT	AGG
(CTG)	 AG	4407-4503	GT	CAG
(GGA)	 AG	4653-4777	GT	AGG
(CTG)	 AG	4858-4970	GT	AGG
(GGT)	 AG	5719-5853	GT	CAG
(GAC)	 AG	6246-6376	GT	GGG
(GTG)	 AG	6740-6893	GT	GGG
(AGG)	 AG	6919-6939	GT	TGG
(GGT)	 AG	6963-6969	GT	AGG
(GTG)	 AG	7004-7137	GT	AGG
-recovered GeneMark_model.107482_t, initial, 1717, 1837
-recovered GeneMark_model.107482_t, internal, 2177, 2340
-recovered GeneMark_model.107482_t, internal, 2708, 2809
-recovered GeneMark_model.107482_t, internal, 3391, 3540
-recovered GeneMark_model.107482_t, internal, 3750, 3900
-recovered GeneMark_model.107482_t, internal, 4104, 4228
-recovered GeneMark_model.107482_t, internal, 4407, 4503
-recovered GeneMark_model.107482_t, internal, 4653, 4777
-recovered GeneMark_model.107482_t, internal, 4858, 4970
-recovered GeneMark_model.107482_t, internal, 5719, 5853
-recovered GeneMark_model.107482_t, internal, 6246, 6376
-recovered GeneMark_model.107482_t, internal, 6740, 6893
-recovered GeneMark_model.107482_t, internal, 6919, 6939
-recovered GeneMark_model.107482_t, internal, 6963, 6969
-recovered GeneMark_model.107482_t, internal, 7004, 7137
Couldn't classify 7004, 7137
Sorry, prediction GlimmerHMM_glimmerT_61776-T1 fails validation.
(ATG)	 CA	893-1013	GT	AGG
(AGC)	 AG	1766-1837	GT	AGG
(AGG)	 AG	2177-2340	GT	AGG
(CTG)	 AG	2708-2809	GT	AGG
(ATC)	 AG	3391-3540	GT	AGG
(GTG)	 AG	3750-3900	GT	TGG
(GGA)	 AG	4104-4228	GT	AGG
(CTG)	 AG	4407-4503	GT	CAG
(GGA)	 AG	4653-4777	GT	AGG
(CTG)	 AG	4858-4970	GT	AGG
(GGT)	 AG	5719-5853	GT	CAG
(GAC)	 AG	6246-6376	GT	GGG
(GTG)	 AG	6740-6876	GT	AGG
(GTG)	 AG	7004-7137	GT	AGG
-recovered GlimmerHMM_glimmerT_61776-T1, initial, 893, 1013
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 1766, 1837
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 2177, 2340
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 2708, 2809
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 3391, 3540
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 3750, 3900
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 4104, 4228
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 4407, 4503
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 4653, 4777
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 4858, 4970
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 5719, 5853
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 6246, 6376
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 6740, 6876
-recovered GlimmerHMM_glimmerT_61776-T1, internal, 7004, 7137
Couldn't classify 7004, 7137
Sorry, prediction Augustus_model.g41057.t1 fails validation.
(ATG)	 CA	893-1013	GT	AGG
(AGG)	 AG	2177-2340	GT	AGG
(CTG)	 AG	2708-2809	GT	AGG
(ATC)	 AG	3391-3540	GT	AGG
(GTG)	 AG	3750-3900	GT	TGG
(GGA)	 AG	4104-4228	GT	AGG
(CTG)	 AG	4407-4458	GT	CAG
(GGA)	 AG	4653-4777	GT	AGG
(CTG)	 AG	4858-4970	GT	AGG
(GGT)	 AG	5719-5853	GT	CAG
(GAC)	 AG	6246-6376	GT	GGG
(GTG)	 AG	6740-6876	GT	AGG
(GTG)	 AG	7004-7137	GT	AGG
-recovered Augustus_model.g41057.t1, initial, 893, 1013
-recovered Augustus_model.g41057.t1, internal, 2177, 2340
-recovered Augustus_model.g41057.t1, internal, 2708, 2809
-recovered Augustus_model.g41057.t1, internal, 3391, 3540
-recovered Augustus_model.g41057.t1, internal, 3750, 3900
-recovered Augustus_model.g41057.t1, internal, 4104, 4228
-recovered Augustus_model.g41057.t1, internal, 4407, 4458
-recovered Augustus_model.g41057.t1, internal, 4653, 4777
-recovered Augustus_model.g41057.t1, internal, 4858, 4970
-recovered Augustus_model.g41057.t1, internal, 5719, 5853
-recovered Augustus_model.g41057.t1, internal, 6246, 6376
-recovered Augustus_model.g41057.t1, internal, 6740, 6876
-recovered Augustus_model.g41057.t1, internal, 7004, 7137
Couldn't classify 303, 485
Couldn't classify 7004, 7135
Sorry, prediction pasa_asmbl_41015.p1 fails validation.
(AAC)	 CC	303-485	GT	AGG
(TGG)	 AG	1714-1837	GT	AGG
(AGG)	 AG	2177-2340	GT	AGG
(CTG)	 AG	2708-2809	GT	AGG
(ATC)	 AG	3391-3540	GT	AGG
(GTG)	 AG	3750-3900	GT	TGG
(GGA)	 AG	4104-4228	GT	AGG
(CTG)	 AG	4407-4519	GT	AGG
(GGT)	 AG	5719-5853	GT	CAG
(GAC)	 AG	6246-6376	GT	GGG
(GTG)	 AG	6740-6876	GT	AGG
(GTG)	 AG	7004-7135	AG	CCA
-recovered pasa_asmbl_41015.p1, internal, 1714, 1837
-recovered pasa_asmbl_41015.p1, internal, 2177, 2340
-recovered pasa_asmbl_41015.p1, internal, 2708, 2809
-recovered pasa_asmbl_41015.p1, internal, 3391, 3540
-recovered pasa_asmbl_41015.p1, internal, 3750, 3900
-recovered pasa_asmbl_41015.p1, internal, 4104, 4228
-recovered pasa_asmbl_41015.p1, internal, 4407, 4519
-recovered pasa_asmbl_41015.p1, internal, 5719, 5853
-recovered pasa_asmbl_41015.p1, internal, 6246, 6376
-recovered pasa_asmbl_41015.p1, internal, 6740, 6876
Couldn't classify 298, 485
Sorry, prediction Augustus_model.g41056.t1 fails validation.
(GAT)	 AG	298-485	GT	AGG
(ACC)	 AG	676-702	TG	AGT
-recovered Augustus_model.g41056.t1, terminal, 676, 702
-recovered Augustus_model.g41056.t1, internal, 298, 485

-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 387, 527
Couldn't classify 7022, 7113
Sorry, prediction snap_scaffold_382-snap.2-T1 fails validation.
(TTG)	 AG	387-527	GT	AGG
(GTT)	 AG	708-835	GT	CTG
(GTA)	 AG	1718-1819	GT	GAG
(GAA)	 AG	5208-5288	GT	CGG
(CCT)	 AG	5700-5869	GT	GGG
(GGC)	 AG	6482-6686	GT	AGG
(GTT)	 AG	7022-7113	GT	ATG
add_exon() Sorry, snap_scaffold_382-snap.2-T1 387-527-terminal-1 is invalid.
-recovered snap_scaffold_382-snap.2-T1, terminal, 387, 527
-recovered snap_scaffold_382-snap.2-T1, internal, 387, 527
-recovered snap_scaffold_382-snap.2-T1, internal, 708, 835
-recovered snap_scaffold_382-snap.2-T1, internal, 1718, 1819
-recovered snap_scaffold_382-snap.2-T1, internal, 5208, 5288
-recovered snap_scaffold_382-snap.2-T1, internal, 5700, 5869
-recovered snap_scaffold_382-snap.2-T1, internal, 6482, 6686
-recovered snap_scaffold_382-snap.2-T1, internal, 7022, 7113
Valid prediction for GeneMark_model.107481_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7137, rend_intergenic: 399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 7511
-exon list size: 45


building trellis

2.1    
4.3    
6.4    
8.5    
10.6    
12.8    
14.9    
17.0    
19.1    
21.3    
23.4    
25.5    
27.7    
29.8    
31.9    
34.0    
36.2    
38.3    
40.4    
42.6    
44.7    
46.8    
48.9    
51.1    
53.2    
55.3    
57.4    
59.6    
61.7    
63.8    
66.0    
68.1    
70.2    
72.3    
74.5    
76.6    
78.7    
80.9    
83.0    
85.1    
87.2    
89.4    
91.5    
93.6    
95.7    
97.9    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 7137, rend_intergenic: 399  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