-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1086

-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 GeneMark_model.108873_t
Valid prediction for GlimmerHMM_glimmerT_62453-T1
Couldn't classify 713, 869
Sorry, prediction snap_scaffold_1086-snap.2-T1 fails validation.
(GGG)	 AG	713-869	GT	TGG
(TGT)	 AG	2151-2539	GT	CGG
(GTA)	 AG	3010-3069	CC	AGC
-recovered snap_scaffold_1086-snap.2-T1, terminal, 3010, 3069
-recovered snap_scaffold_1086-snap.2-T1, internal, 713, 869
-recovered snap_scaffold_1086-snap.2-T1, internal, 2151, 2539

-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 3198, 3286
Sorry, prediction GeneMark_model.108872_t fails validation.
(ATG)	 TG	1275-1285	GT	GTG
(GGG)	 AG	1318-1451	GT	AGG
(CGG)	 AG	1723-1744	GT	ATG
(ACC)	 AG	1875-2009	GT	CAG
(GGA)	 AG	2077-2091	GT	GAG
(AGT)	 AG	2514-2598	GT	CTG
(GGG)	 AG	3198-3286	GT	AAG
-recovered GeneMark_model.108872_t, initial, 1275, 1285
-recovered GeneMark_model.108872_t, terminal, 2077, 2091
-recovered GeneMark_model.108872_t, internal, 1318, 1451
-recovered GeneMark_model.108872_t, internal, 1723, 1744
-recovered GeneMark_model.108872_t, internal, 1875, 2009
-recovered GeneMark_model.108872_t, internal, 2077, 2091
-recovered GeneMark_model.108872_t, internal, 2514, 2598
-recovered GeneMark_model.108872_t, internal, 3198, 3286
Couldn't classify 222, 335
Sorry, prediction GlimmerHMM_glimmerT_62454-T1 fails validation.
(CGG)	 AG	222-335	GT	AGG
(GGA)	 AG	635-766	GT	AGG
(CCC)	 AG	1266-1451	GT	AGG
(CGG)	 AG	1723-1793	CA	AAC
-recovered GlimmerHMM_glimmerT_62454-T1, terminal, 1723, 1793
-recovered GlimmerHMM_glimmerT_62454-T1, internal, 222, 335
-recovered GlimmerHMM_glimmerT_62454-T1, internal, 635, 766
-recovered GlimmerHMM_glimmerT_62454-T1, internal, 1266, 1451
Couldn't classify 3198, 3286
Sorry, prediction Augustus_model.g41516.t1 fails validation.
(ATG)	 AG	236-335	GT	AGG
(GGA)	 AG	635-766	GT	AGG
(GTA)	 AG	1105-1170	GT	TGG
(CCC)	 AG	1266-1451	GT	AGG
(GCG)	 AG	1831-1991	GT	AAG
(TCT)	 AG	2500-2598	GT	CTG
(GGG)	 AG	3198-3286	GT	AAG
-recovered Augustus_model.g41516.t1, initial, 236, 335
-recovered Augustus_model.g41516.t1, internal, 236, 335
-recovered Augustus_model.g41516.t1, internal, 635, 766
-recovered Augustus_model.g41516.t1, internal, 1105, 1170
-recovered Augustus_model.g41516.t1, internal, 1266, 1451
-recovered Augustus_model.g41516.t1, internal, 1831, 1991
-recovered Augustus_model.g41516.t1, internal, 2500, 2598
-recovered Augustus_model.g41516.t1, internal, 3198, 3286
Couldn't classify 3198, 3286
Sorry, prediction snap_scaffold_1086-snap.1-T1 fails validation.
(ATG)	 AG	236-335	GT	AGG
(GTA)	 AG	1105-1170	GT	TGG
(CCC)	 AG	1266-1451	GT	AGG
(GCG)	 AG	1831-1991	GT	AAG
(TCT)	 AG	2500-2598	GT	CTG
(GGG)	 AG	3198-3286	GT	AAG
-recovered snap_scaffold_1086-snap.1-T1, initial, 236, 335
-recovered snap_scaffold_1086-snap.1-T1, internal, 236, 335
-recovered snap_scaffold_1086-snap.1-T1, internal, 1105, 1170
-recovered snap_scaffold_1086-snap.1-T1, internal, 1266, 1451
-recovered snap_scaffold_1086-snap.1-T1, internal, 1831, 1991
-recovered snap_scaffold_1086-snap.1-T1, internal, 2500, 2598
-recovered snap_scaffold_1086-snap.1-T1, internal, 3198, 3286
Valid prediction for GeneMark_model.108874_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3093, rend_intergenic: 713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 3328
-exon list size: 37


building trellis

2.6    
5.1    
7.7    
10.3    
12.8    
15.4    
17.9    
20.5    
23.1    
25.6    
28.2    
30.8    
33.3    
35.9    
38.5    
41.0    
43.6    
46.2    
48.7    
51.3    
53.8    
56.4    
59.0    
61.5    
64.1    
66.7    
69.2    
71.8    
74.4    
76.9    
79.5    
82.1    
84.6    
87.2    
89.7    
92.3    
94.9    
97.4    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 3093, rend_intergenic: 713  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