-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_654

-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 96, 254
Sorry, prediction snap_scaffold_654-snap.1-T1 fails validation.
(GTG)	 AG	96-254	GT	GGG
(GTG)	 AG	703-814	GT	GGG
(GTA)	 AG	1256-1578	GT	GGG
(GTG)	 AG	1764-2291	GT	GGG
(GTG)	 AG	2342-2459	GT	AGG
(GTA)	 AG	3793-4007	AA	GAA
-recovered snap_scaffold_654-snap.1-T1, terminal, 3793, 4007
-recovered snap_scaffold_654-snap.1-T1, internal, 96, 254
-recovered snap_scaffold_654-snap.1-T1, internal, 703, 814
-recovered snap_scaffold_654-snap.1-T1, internal, 1256, 1578
-recovered snap_scaffold_654-snap.1-T1, internal, 1764, 2291
-recovered snap_scaffold_654-snap.1-T1, internal, 2342, 2459
Couldn't classify 96, 254
Sorry, prediction Augustus_model.g40109.t1 fails validation.
(GTG)	 AG	96-254	GT	GGG
(GTG)	 AG	703-814	GT	GGG
(GTA)	 AG	1256-1374	GT	AGG
(GTG)	 AG	1764-1973	GT	AGG
(GTG)	 AG	2342-2494	CA	AAC
-recovered Augustus_model.g40109.t1, terminal, 2342, 2494
-recovered Augustus_model.g40109.t1, internal, 96, 254
-recovered Augustus_model.g40109.t1, internal, 703, 814
-recovered Augustus_model.g40109.t1, internal, 1256, 1374
-recovered Augustus_model.g40109.t1, internal, 1764, 1973
Couldn't classify 96, 254
Couldn't classify 2342, 2458
Sorry, prediction pasa_asmbl_49501.p1 fails validation.
(GTG)	 AG	96-254	GT	GGG
(GTG)	 AG	703-814	GT	GGG
(GTA)	 AG	1256-1374	GT	AGG
(GTG)	 AG	1764-1973	GT	AGG
(GTG)	 AG	2342-2458	GG	CAG
-recovered pasa_asmbl_49501.p1, internal, 96, 254
-recovered pasa_asmbl_49501.p1, internal, 703, 814
-recovered pasa_asmbl_49501.p1, internal, 1256, 1374
-recovered pasa_asmbl_49501.p1, internal, 1764, 1973
Valid prediction for GlimmerHMM_glimmerT_60589-T1
Valid prediction for GlimmerHMM_glimmerT_60590-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: -)Valid prediction for Augustus_model.g40110.t1
Couldn't classify 986, 1100
Couldn't classify 3789, 3855
Sorry, prediction snap_scaffold_654-snap.2-T1 fails validation.
(TGT)	 AG	986-1100	GT	GTG
(CTG)	 AG	1112-1357	GT	ACG
(GGC)	 AG	3116-3171	GT	AGG
(GTT)	 AG	3789-3855	GT	AGG
-recovered snap_scaffold_654-snap.2-T1, internal, 986, 1100
-recovered snap_scaffold_654-snap.2-T1, internal, 1112, 1357
-recovered snap_scaffold_654-snap.2-T1, internal, 3116, 3171
-recovered snap_scaffold_654-snap.2-T1, internal, 3789, 3855
Valid prediction for GlimmerHMM_glimmerT_60591-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4007, rend_intergenic: 1260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 5114
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 4007, rend_intergenic: 1260  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