-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_643

-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 1194, 1301
Sorry, prediction snap_scaffold_643-snap.2-T1 fails validation.
(CAA)	 AG	1194-1301	GT	AAG
(GGT)	 AG	1520-1568	GT	AGG
(ATG)	 AG	1942-2037	GT	CGG
(ATA)	 AG	2620-2784	CG	GAC
-recovered snap_scaffold_643-snap.2-T1, initial, 1942, 2037
-recovered snap_scaffold_643-snap.2-T1, terminal, 2620, 2784
-recovered snap_scaffold_643-snap.2-T1, internal, 1194, 1301
-recovered snap_scaffold_643-snap.2-T1, internal, 1520, 1568
-recovered snap_scaffold_643-snap.2-T1, internal, 1942, 2037
Valid prediction for GeneMark_model.108115_t

-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 2390, 2664
Couldn't classify 5059, 5206
Sorry, prediction snap_scaffold_643-snap.1-T1 fails validation.
(TGA)	 AG	2390-2664	GT	AGG
(GTG)	 AG	3117-3289	GT	AGG
(AGA)	 AG	3743-3843	GT	CGG
(CAT)	 AG	3926-4091	GT	AGG
(AGA)	 AG	5059-5206	GT	TGG
-recovered snap_scaffold_643-snap.1-T1, internal, 2390, 2664
-recovered snap_scaffold_643-snap.1-T1, internal, 3117, 3289
-recovered snap_scaffold_643-snap.1-T1, internal, 3743, 3843
-recovered snap_scaffold_643-snap.1-T1, internal, 3926, 4091
-recovered snap_scaffold_643-snap.1-T1, internal, 5059, 5206
Couldn't classify 2365, 2664
Couldn't classify 3926, 4092
Sorry, prediction pasa_asmbl_49428.p1 fails validation.
(CCC)	 CA	2365-2664	GT	AGG
(GTG)	 AG	3117-3289	GT	AGG
(AGA)	 AG	3743-3843	GT	CGG
(CAT)	 AG	3926-4092	TA	GGT
-recovered pasa_asmbl_49428.p1, internal, 3117, 3289
-recovered pasa_asmbl_49428.p1, internal, 3743, 3843
Couldn't classify 2390, 2664
Sorry, prediction GlimmerHMM_glimmerT_62077-T1 fails validation.
(TGA)	 AG	2390-2664	GT	AGG
(GGT)	 AG	3131-3172	GG	GAG
-recovered GlimmerHMM_glimmerT_62077-T1, terminal, 3131, 3172
-recovered GlimmerHMM_glimmerT_62077-T1, internal, 2390, 2664
Valid prediction for Augustus_model.g41265.t1
Couldn't classify 5077, 5187
Sorry, prediction GeneMark_model.108114_t fails validation.
(ATG)	 CC	2473-2664	GT	AGG
(GTG)	 AG	3117-3261	GT	CTG
(CAT)	 AG	3926-4091	GT	AGG
(AGA)	 AG	4304-4324	GT	GTG
(AGA)	 AG	4353-4364	GT	AGG
(AGA)	 AG	4453-4482	GT	AGG
(ACA)	 AG	4531-4575	GT	GAG
(AGC)	 AG	4876-4881	GC	GGG
(AGA)	 AG	4907-4945	GT	GAG
(AGG)	 AG	4968-5003	GC	AGG
(AAA)	 AG	5025-5033	GT	GTG
(TCC)	 AG	5077-5187	GC	AAG
-recovered GeneMark_model.108114_t, initial, 2473, 2664
-recovered GeneMark_model.108114_t, internal, 3117, 3261
-recovered GeneMark_model.108114_t, internal, 3926, 4091
-recovered GeneMark_model.108114_t, internal, 4304, 4324
-recovered GeneMark_model.108114_t, internal, 4353, 4364
-recovered GeneMark_model.108114_t, internal, 4453, 4482
-recovered GeneMark_model.108114_t, internal, 4531, 4575
-recovered GeneMark_model.108114_t, internal, 4876, 4881
-recovered GeneMark_model.108114_t, internal, 4907, 4945
-recovered GeneMark_model.108114_t, internal, 4968, 5003
-recovered GeneMark_model.108114_t, internal, 5025, 5033
-recovered GeneMark_model.108114_t, internal, 5077, 5187

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 2824, rend_intergenic: 1194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 5213
-exon list size: 42


building trellis

2.3    
4.5    
6.8    
9.1    
11.4    
13.6    
15.9    
18.2    
20.5    
22.7    
25.0    
27.3    
29.5    
31.8    
34.1    
36.4    
38.6    
40.9    
43.2    
45.5    
47.7    
50.0    
52.3    
54.5    
56.8    
59.1    
61.4    
63.6    
65.9    
68.2    
70.5    
72.7    
75.0    
77.3    
79.5    
81.8    
84.1    
86.4    
88.6    
90.9    
93.2    
95.5    
97.7    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 2824, rend_intergenic: 1194  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