-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_518

-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: +)Valid prediction for snap_scaffold_518-snap.1-T1
Couldn't classify 39, 59
Sorry, prediction GeneMark_model.107844_t fails validation.
(AGG)	 AG	39-59	GT	CAG
(AGA)	 AG	157-174	GT	AAG
(AGA)	 AG	1212-1352	GT	AAG
(GGA)	 AG	2036-2044	GT	GGG
(AGA)	 AG	2069-2129	GT	ACG
(AGA)	 AG	2153-2163	GT	GAG
(AGA)	 AG	2219-2233	GT	CGG
(GGG)	 AG	2293-2421	GT	GAG
(AGA)	 AG	4485-4499	GT	GGG
(GGT)	 AG	4524-4550	GT	GGG
(GGT)	 AG	4575-4601	GT	GGG
(GAT)	 AG	4622-4636	GT	TTG
(AGA)	 AG	4700-4765	GC	AGG
(ACA)	 AG	4792-4977	GT	GAG
(GTA)	 AG	5035-5121	GT	CAG
(AGA)	 AG	5287-5295	GT	GAG
(AGT)	 AG	5376-5394	GA	GAG
-recovered GeneMark_model.107844_t, terminal, 5376, 5394
-recovered GeneMark_model.107844_t, internal, 39, 59
-recovered GeneMark_model.107844_t, internal, 157, 174
-recovered GeneMark_model.107844_t, internal, 1212, 1352
-recovered GeneMark_model.107844_t, internal, 2036, 2044
-recovered GeneMark_model.107844_t, internal, 2069, 2129
-recovered GeneMark_model.107844_t, internal, 2153, 2163
-recovered GeneMark_model.107844_t, internal, 2219, 2233
-recovered GeneMark_model.107844_t, internal, 2293, 2421
-recovered GeneMark_model.107844_t, internal, 4485, 4499
-recovered GeneMark_model.107844_t, internal, 4524, 4550
-recovered GeneMark_model.107844_t, internal, 4575, 4601
-recovered GeneMark_model.107844_t, internal, 4622, 4636
-recovered GeneMark_model.107844_t, internal, 4700, 4765
-recovered GeneMark_model.107844_t, internal, 4792, 4977
-recovered GeneMark_model.107844_t, internal, 5035, 5121
-recovered GeneMark_model.107844_t, internal, 5287, 5295
Valid prediction for snap_scaffold_518-snap.2-T1

-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 105, 166
Sorry, prediction GlimmerHMM_glimmerT_61948-T1 fails validation.
(ACC)	 AG	105-166	GT	GGG
(GGC)	 AG	582-790	GT	AGG
(GCG)	 AG	1100-1238	GT	AAG
(GAA)	 AG	3430-3442	AC	GAA
-recovered GlimmerHMM_glimmerT_61948-T1, terminal, 3430, 3442
-recovered GlimmerHMM_glimmerT_61948-T1, internal, 105, 166
-recovered GlimmerHMM_glimmerT_61948-T1, internal, 582, 790
-recovered GlimmerHMM_glimmerT_61948-T1, internal, 1100, 1238
Couldn't classify 5048, 5240
Sorry, prediction pasa_asmbl_46473.p1 fails validation.
(ATG)	 GG	3454-3644	GT	GGG
(GTG)	 AG	5048-5240	AC	GTA
-recovered pasa_asmbl_46473.p1, initial, 3454, 3644
Couldn't classify 37, 81
Sorry, prediction GeneMark_model.107845_t fails validation.
(AGG)	 AG	37-81	GT	TCG
(ACC)	 AG	105-166	GT	GGG
(GGC)	 AG	582-798	AC	AAA
-recovered GeneMark_model.107845_t, terminal, 582, 798
-recovered GeneMark_model.107845_t, internal, 37, 81
-recovered GeneMark_model.107845_t, internal, 105, 166
Valid prediction for GlimmerHMM_glimmerT_61947-T1
Couldn't classify 105, 166
Couldn't classify 5048, 5238
Sorry, prediction Augustus_model.g41175.t1 fails validation.
(ACC)	 AG	105-166	GT	GGG
(GGC)	 AG	582-790	GT	AGG
(GCG)	 AG	1100-1238	GT	AAG
(GAT)	 AG	3453-3644	GT	GGG
(GTG)	 AG	5048-5238	GT	AGG
-recovered Augustus_model.g41175.t1, internal, 105, 166
-recovered Augustus_model.g41175.t1, internal, 582, 790
-recovered Augustus_model.g41175.t1, internal, 1100, 1238
-recovered Augustus_model.g41175.t1, internal, 3453, 3644
-recovered Augustus_model.g41175.t1, internal, 5048, 5238
Couldn't classify 78, 166
Sorry, prediction snap_scaffold_518-snap.3-T1 fails validation.
(AGT)	 AG	78-166	GT	GGG
(GGC)	 AG	582-790	GT	AGG
(GCG)	 AG	1100-1238	GT	AAG
(GAT)	 AG	2313-2328	TT	GAT
-recovered snap_scaffold_518-snap.3-T1, terminal, 2313, 2328
-recovered snap_scaffold_518-snap.3-T1, internal, 78, 166
-recovered snap_scaffold_518-snap.3-T1, internal, 582, 790
-recovered snap_scaffold_518-snap.3-T1, internal, 1100, 1238

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5702, rend_intergenic: 3901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 6228
-exon list size: 64


building trellis

1.5    
3.0    
4.5    
6.1    
7.6    
9.1    
10.6    
12.1    
13.6    
15.2    
16.7    
18.2    
19.7    
21.2    
22.7    
24.2    
25.8    
27.3    
28.8    
30.3    
31.8    
33.3    
34.8    
36.4    
37.9    
39.4    
40.9    
42.4    
43.9    
45.5    
47.0    
48.5    
50.0    
51.5    
53.0    
54.5    
56.1    
57.6    
59.1    
60.6    
62.1    
63.6    
65.2    
66.7    
68.2    
69.7    
71.2    
72.7    
74.2    
75.8    
77.3    
78.8    
80.3    
81.8    
83.3    
84.8    
86.4    
87.9    
89.4    
90.9    
92.4    
93.9    
95.5    
97.0    
98.5    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 5702, rend_intergenic: 3901  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