-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_662

-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 1179, 1454
Sorry, prediction snap_scaffold_662-snap.1-T1 fails validation.
(AGA)	 AG	1179-1454	GT	GGG
(CCC)	 AG	2069-2326	GT	ATG
(ACG)	 AG	2803-2919	CA	AAC
-recovered snap_scaffold_662-snap.1-T1, terminal, 2803, 2919
-recovered snap_scaffold_662-snap.1-T1, internal, 1179, 1454
-recovered snap_scaffold_662-snap.1-T1, internal, 2069, 2326
Valid prediction for snap_scaffold_662-snap.3-T1
Valid prediction for GeneMark_model.108152_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 998, 1229
Couldn't classify 3481, 3717
Sorry, prediction snap_scaffold_662-snap.2-T1 fails validation.
(GTC)	 AG	998-1229	GT	AGG
(GCT)	 AG	1739-1849	GT	AGG
(GTG)	 AG	1941-2135	GT	AGG
(ATG)	 AG	2566-2672	GT	AGG
(GGC)	 AG	3009-3135	GT	AGG
(ATG)	 AG	3481-3717	GT	AGG
-recovered snap_scaffold_662-snap.2-T1, initial, 2566, 2672
-recovered snap_scaffold_662-snap.2-T1, initial, 3481, 3717
-recovered snap_scaffold_662-snap.2-T1, internal, 998, 1229
-recovered snap_scaffold_662-snap.2-T1, internal, 1739, 1849
-recovered snap_scaffold_662-snap.2-T1, internal, 1941, 2135
-recovered snap_scaffold_662-snap.2-T1, internal, 2566, 2672
-recovered snap_scaffold_662-snap.2-T1, internal, 3009, 3135
-recovered snap_scaffold_662-snap.2-T1, internal, 3481, 3717
Couldn't classify 998, 1229
Sorry, prediction Augustus_model.g41282.t1 fails validation.
(GTC)	 AG	998-1229	GT	AGG
(GCT)	 AG	1739-1849	GT	AGG
(GTG)	 AG	1941-2135	GT	AGG
(ATG)	 AG	2566-2672	GT	AGG
(GGC)	 AG	3009-3135	GT	AGG
(ATG)	 AG	3481-3747	TG	GAT
-recovered Augustus_model.g41282.t1, initial, 2566, 2672
-recovered Augustus_model.g41282.t1, terminal, 3481, 3747
-recovered Augustus_model.g41282.t1, internal, 998, 1229
-recovered Augustus_model.g41282.t1, internal, 1739, 1849
-recovered Augustus_model.g41282.t1, internal, 1941, 2135
-recovered Augustus_model.g41282.t1, internal, 2566, 2672
-recovered Augustus_model.g41282.t1, internal, 3009, 3135
Couldn't classify 4871, 4981
Sorry, prediction GeneMark_model.108151_t fails validation.
(ATG)	 CC	3589-3740	GT	GGG
(GAT)	 AG	3917-3937	GT	GAG
(AGA)	 AG	3961-3969	GT	GAG
(AAA)	 AG	3991-4017	GT	GAG
(AGA)	 AG	4041-4049	GT	GAG
(GGT)	 AG	4071-4214	GT	GGG
(AGA)	 AG	4615-4623	GT	GTG
(AGA)	 AG	4649-4663	GT	GTG
(AGA)	 AG	4687-4695	GT	GTG
(AGA)	 AG	4717-4731	GT	ATG
(AGA)	 AG	4759-4773	GT	GTG
(AGA)	 AG	4799-4807	GT	ATG
(AGA)	 AG	4833-4847	GT	ATG
(TGA)	 AG	4871-4981	GT	AGG
-recovered GeneMark_model.108151_t, initial, 3589, 3740
add_exon() Sorry, GeneMark_model.108151_t 3917-3937-terminal-1 is invalid.
-recovered GeneMark_model.108151_t, terminal, 3917, 3937
-recovered GeneMark_model.108151_t, terminal, 3961, 3969
add_exon() Sorry, GeneMark_model.108151_t 3991-4017-terminal-1 is invalid.
-recovered GeneMark_model.108151_t, terminal, 3991, 4017
-recovered GeneMark_model.108151_t, terminal, 4041, 4049
-recovered GeneMark_model.108151_t, internal, 3917, 3937
-recovered GeneMark_model.108151_t, internal, 3961, 3969
-recovered GeneMark_model.108151_t, internal, 3991, 4017
-recovered GeneMark_model.108151_t, internal, 4041, 4049
-recovered GeneMark_model.108151_t, internal, 4071, 4214
-recovered GeneMark_model.108151_t, internal, 4615, 4623
-recovered GeneMark_model.108151_t, internal, 4649, 4663
-recovered GeneMark_model.108151_t, internal, 4687, 4695
-recovered GeneMark_model.108151_t, internal, 4717, 4731
-recovered GeneMark_model.108151_t, internal, 4759, 4773
-recovered GeneMark_model.108151_t, internal, 4799, 4807
-recovered GeneMark_model.108151_t, internal, 4833, 4847
-recovered GeneMark_model.108151_t, internal, 4871, 4981
Couldn't classify 998, 1229
Sorry, prediction GlimmerHMM_glimmerT_62100-T1 fails validation.
(GTC)	 AG	998-1229	GT	AGG
(GCT)	 AG	1739-1849	GT	AGG
(GTG)	 AG	1941-2135	GT	AGG
(ATG)	 AG	2566-2672	GT	AGG
(GGC)	 AG	3009-3135	GT	AGG
(ATG)	 AG	3481-3747	TG	GAT
-recovered GlimmerHMM_glimmerT_62100-T1, initial, 2566, 2672
-recovered GlimmerHMM_glimmerT_62100-T1, terminal, 3481, 3747
-recovered GlimmerHMM_glimmerT_62100-T1, internal, 998, 1229
-recovered GlimmerHMM_glimmerT_62100-T1, internal, 1739, 1849
-recovered GlimmerHMM_glimmerT_62100-T1, internal, 1941, 2135
-recovered GlimmerHMM_glimmerT_62100-T1, internal, 2566, 2672
-recovered GlimmerHMM_glimmerT_62100-T1, internal, 3009, 3135
Couldn't classify 1008, 1229
Couldn't classify 3481, 3717
Sorry, prediction pasa_asmbl_49448.p1 fails validation.
(GCA)	 AG	1008-1229	GT	AGG
(GCT)	 AG	1739-1849	GT	AGG
(GTG)	 AG	1941-2135	GT	AGG
(ATG)	 AG	2566-2672	GT	AGG
(GGC)	 AG	3009-3135	GT	AGG
(ATG)	 AG	3481-3717	GT	AGG
-recovered pasa_asmbl_49448.p1, initial, 2566, 2672
-recovered pasa_asmbl_49448.p1, initial, 3481, 3717
-recovered pasa_asmbl_49448.p1, internal, 1008, 1229
-recovered pasa_asmbl_49448.p1, internal, 1739, 1849
-recovered pasa_asmbl_49448.p1, internal, 1941, 2135
-recovered pasa_asmbl_49448.p1, internal, 2566, 2672
-recovered pasa_asmbl_49448.p1, internal, 3009, 3135
-recovered pasa_asmbl_49448.p1, internal, 3481, 3717
Couldn't classify 677, 684
Sorry, prediction GeneMark_model.108153_t fails validation.
(CCT)	 AG	677-684	GT	AGG
(CTT)	 AG	963-1229	GT	AGG
(GCT)	 AG	1739-1849	GT	AGG
(GTG)	 AG	1941-2135	GT	AGG
(ATG)	 AG	2566-2676	GA	AAG
-recovered GeneMark_model.108153_t, terminal, 2566, 2676
-recovered GeneMark_model.108153_t, internal, 677, 684
-recovered GeneMark_model.108153_t, internal, 963, 1229
-recovered GeneMark_model.108153_t, internal, 1739, 1849
-recovered GeneMark_model.108153_t, internal, 1941, 2135

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 2919, rend_intergenic: 1362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 4081, rend_intergenic: 2971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 5078
-exon list size: 65


building trellis

1.5    
3.0    
4.5    
6.0    
7.5    
9.0    
10.4    
11.9    
13.4    
14.9    
16.4    
17.9    
19.4    
20.9    
22.4    
23.9    
25.4    
26.9    
28.4    
29.9    
31.3    
32.8    
34.3    
35.8    
37.3    
38.8    
40.3    
41.8    
43.3    
44.8    
46.3    
47.8    
49.3    
50.7    
52.2    
53.7    
55.2    
56.7    
58.2    
59.7    
61.2    
62.7    
64.2    
65.7    
67.2    
68.7    
70.1    
71.6    
73.1    
74.6    
76.1    
77.6    
79.1    
80.6    
82.1    
83.6    
85.1    
86.6    
88.1    
89.6    
91.0    
92.5    
94.0    
95.5    
97.0    
98.5    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 2919, rend_intergenic: 1362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 4081, rend_intergenic: 2971  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