-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1022

-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 160, 300
Couldn't classify 2952, 3085
Sorry, prediction snap_scaffold_1022-snap.2-T1 fails validation.
(TCT)	 AG	160-300	GT	AGG
(TCG)	 AG	2425-2479	GT	TGG
(CCA)	 AG	2952-3085	GT	GAG
-recovered snap_scaffold_1022-snap.2-T1, internal, 160, 300
-recovered snap_scaffold_1022-snap.2-T1, internal, 2425, 2479
-recovered snap_scaffold_1022-snap.2-T1, internal, 2952, 3085

-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, 341
Sorry, prediction GlimmerHMM_glimmerT_62410-T1 fails validation.
(GCT)	 AG	105-341	GT	AGG
(GGG)	 AG	487-618	GT	AGG
(GCG)	 AG	1060-1176	GT	AGG
(TGT)	 AG	2782-2882	GT	GTG
(GCT)	 AG	3244-3252	GC	GAG
-recovered GlimmerHMM_glimmerT_62410-T1, terminal, 3244, 3252
-recovered GlimmerHMM_glimmerT_62410-T1, internal, 105, 341
-recovered GlimmerHMM_glimmerT_62410-T1, internal, 487, 618
-recovered GlimmerHMM_glimmerT_62410-T1, internal, 1060, 1176
-recovered GlimmerHMM_glimmerT_62410-T1, internal, 2782, 2882
-recovered GlimmerHMM_glimmerT_62410-T1, internal, 3244, 3252
Couldn't classify 105, 341
Couldn't classify 3244, 3495
Sorry, prediction Augustus_model.g41485.t1 fails validation.
(GCT)	 AG	105-341	GT	AGG
(GGG)	 AG	487-618	GT	AGG
(GCG)	 AG	1060-1176	GT	AGG
(TGT)	 AG	2782-2901	GT	AGG
(GCT)	 AG	3244-3495	GT	TGG
-recovered Augustus_model.g41485.t1, internal, 105, 341
-recovered Augustus_model.g41485.t1, internal, 487, 618
-recovered Augustus_model.g41485.t1, internal, 1060, 1176
-recovered Augustus_model.g41485.t1, internal, 2782, 2901
-recovered Augustus_model.g41485.t1, internal, 3244, 3495
Valid prediction for CodingQuarry_transcript_5691-T1
Couldn't classify 105, 341
Couldn't classify 3244, 3495
Sorry, prediction snap_scaffold_1022-snap.1-T1 fails validation.
(GCT)	 AG	105-341	GT	AGG
(GGG)	 AG	487-618	GT	AGG
(GCG)	 AG	1060-1176	GT	AGG
(TGT)	 AG	2782-2901	GT	AGG
(GCT)	 AG	3244-3495	GT	TGG
-recovered snap_scaffold_1022-snap.1-T1, internal, 105, 341
-recovered snap_scaffold_1022-snap.1-T1, internal, 487, 618
-recovered snap_scaffold_1022-snap.1-T1, internal, 1060, 1176
-recovered snap_scaffold_1022-snap.1-T1, internal, 2782, 2901
-recovered snap_scaffold_1022-snap.1-T1, internal, 3244, 3495
Couldn't classify 2787, 2901
Couldn't classify 3244, 3494
Sorry, prediction pasa_asmbl_5187.p1 fails validation.
(AGG)	 AC	2787-2901	GT	AGG
(GCT)	 AG	3244-3494	GG	ATG
Couldn't classify 43, 71
Couldn't classify 3244, 3495
Sorry, prediction GeneMark_model.108772_t fails validation.
(TGC)	 AG	43-71	GT	TGG
(GCT)	 AG	105-341	GT	AGG
(GGG)	 AG	487-618	GT	AGG
(GCG)	 AG	1060-1176	GT	AGG
(GAT)	 AG	1238-1247	GT	AGG
(GGG)	 AG	2636-2701	GT	GCG
(GCT)	 AG	2789-2901	GT	AGG
(GCT)	 AG	3244-3495	GT	TGG
-recovered GeneMark_model.108772_t, internal, 43, 71
-recovered GeneMark_model.108772_t, internal, 105, 341
-recovered GeneMark_model.108772_t, internal, 487, 618
-recovered GeneMark_model.108772_t, internal, 1060, 1176
-recovered GeneMark_model.108772_t, internal, 1238, 1247
-recovered GeneMark_model.108772_t, internal, 2636, 2701
-recovered GeneMark_model.108772_t, internal, 2789, 2901
-recovered GeneMark_model.108772_t, internal, 3244, 3495
Couldn't classify 53, 341
Couldn't classify 1060, 1175
Sorry, prediction pasa_asmbl_5186.p1 fails validation.
(GTG)	 GT	53-341	GT	AGG
(GGG)	 AG	487-618	GT	AGG
(GCG)	 AG	1060-1175	GG	CAG
-recovered pasa_asmbl_5186.p1, internal, 487, 618

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3444, rend_intergenic: 160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 3548
-exon list size: 23


building trellis

4.0    
8.0    
12.0    
16.0    
20.0    
24.0    
28.0    
32.0    
36.0    
40.0    
44.0    
48.0    
52.0    
56.0    
60.0    
64.0    
68.0    
72.0    
76.0    
80.0    
84.0    
88.0    
92.0    
96.0    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 3444, rend_intergenic: 160  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