-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/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: +)Valid prediction for GlimmerHMM_glimmerT_62091-T1
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
Valid prediction for GlimmerHMM_glimmerT_62092-T1
Couldn't classify 96, 254
Couldn't classify 2342, 2458
Sorry, prediction pasa_asmbl_49439.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_49439.p1, internal, 96, 254
-recovered pasa_asmbl_49439.p1, internal, 703, 814
-recovered pasa_asmbl_49439.p1, internal, 1256, 1374
-recovered pasa_asmbl_49439.p1, internal, 1764, 1973
Couldn't classify 96, 254
Sorry, prediction GeneMark_model.108139_t fails validation.
(GTG)	 AG	96-254	GT	GGG
(GTG)	 AG	703-814	GT	GGG
(GTA)	 AG	1256-1511	GT	GGG
(GTC)	 AG	1547-1682	GT	AGG
(GTG)	 AG	1764-2297	GT	GCG
(GTG)	 AG	2342-2459	GT	AGG
(GCC)	 AG	3613-3638	GG	GAG
-recovered GeneMark_model.108139_t, terminal, 3613, 3638
-recovered GeneMark_model.108139_t, internal, 96, 254
-recovered GeneMark_model.108139_t, internal, 703, 814
-recovered GeneMark_model.108139_t, internal, 1256, 1511
-recovered GeneMark_model.108139_t, internal, 1547, 1682
-recovered GeneMark_model.108139_t, internal, 1764, 2297
-recovered GeneMark_model.108139_t, internal, 2342, 2459
Couldn't classify 96, 254
Sorry, prediction Augustus_model.g41274.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.g41274.t1, terminal, 2342, 2494
-recovered Augustus_model.g41274.t1, internal, 96, 254
-recovered Augustus_model.g41274.t1, internal, 703, 814
-recovered Augustus_model.g41274.t1, internal, 1256, 1374
-recovered Augustus_model.g41274.t1, internal, 1764, 1973

-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 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_62093-T1
Couldn't classify 1023, 1083
Sorry, prediction GeneMark_model.108140_t fails validation.
(TGC)	 AG	1023-1083	GT	AGG
(CTG)	 AG	1112-1399	AG	AAA
-recovered GeneMark_model.108140_t, terminal, 1112, 1399
-recovered GeneMark_model.108140_t, internal, 1023, 1083
Valid prediction for Augustus_model.g41275.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: 33


building trellis

2.9    
5.7    
8.6    
11.4    
14.3    
17.1    
20.0    
22.9    
25.7    
28.6    
31.4    
34.3    
37.1    
40.0    
42.9    
45.7    
48.6    
51.4    
54.3    
57.1    
60.0    
62.9    
65.7    
68.6    
71.4    
74.3    
77.1    
80.0    
82.9    
85.7    
88.6    
91.4    
94.3    
97.1    
-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