-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_479

-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.107749_t
Valid prediction for GeneMark_model.107750_t
Couldn't classify 1613, 1709
Couldn't classify 5675, 5834
Sorry, prediction snap_scaffold_479-snap.3-T1 fails validation.
(ATC)	 AG	1613-1709	GT	AGG
(GCT)	 AG	3162-3237	GT	AAG
(CCA)	 AG	3703-3978	GT	AGG
(GTG)	 AG	4188-4862	GT	ACG
(AGG)	 AG	5675-5834	GT	AGG
-recovered snap_scaffold_479-snap.3-T1, internal, 1613, 1709
-recovered snap_scaffold_479-snap.3-T1, internal, 3162, 3237
-recovered snap_scaffold_479-snap.3-T1, internal, 3703, 3978
-recovered snap_scaffold_479-snap.3-T1, internal, 4188, 4862
-recovered snap_scaffold_479-snap.3-T1, internal, 5675, 5834

-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 6419, 6476
Sorry, prediction GeneMark_model.107747_t fails validation.
(ATG)	 GA	5883-5890	GT	TGG
(GTG)	 AG	5990-6092	GT	ATG
(GCA)	 AG	6419-6476	GT	TGG
-recovered GeneMark_model.107747_t, initial, 5883, 5890
-recovered GeneMark_model.107747_t, internal, 5990, 6092
-recovered GeneMark_model.107747_t, internal, 6419, 6476
Couldn't classify 790, 971
Sorry, prediction GlimmerHMM_glimmerT_61899-T1 fails validation.
(GTA)	 AG	790-971	GT	TGG
(GGT)	 AG	2918-3208	GT	GGG
(TGC)	 AG	5108-5539	AC	GAA
-recovered GlimmerHMM_glimmerT_61899-T1, terminal, 5108, 5539
-recovered GlimmerHMM_glimmerT_61899-T1, internal, 790, 971
-recovered GlimmerHMM_glimmerT_61899-T1, internal, 2918, 3208
Valid prediction for GeneMark_model.107752_t
add_exon() Sorry, GeneMark_model.107752_t 790-1019-terminal-1 is invalid.
Valid prediction for GlimmerHMM_glimmerT_61898-T1
Couldn't classify 248, 294
Couldn't classify 6419, 6476
Sorry, prediction Augustus_model.g41146.t1 fails validation.
(AAC)	 AG	248-294	GT	TGG
(GTA)	 AG	790-971	GT	TGG
(GGT)	 AG	2918-3045	GT	CGG
(GTG)	 AG	5990-6092	GT	ATG
(GCA)	 AG	6419-6476	GT	TGG
-recovered Augustus_model.g41146.t1, internal, 248, 294
-recovered Augustus_model.g41146.t1, internal, 790, 971
-recovered Augustus_model.g41146.t1, internal, 2918, 3045
-recovered Augustus_model.g41146.t1, internal, 5990, 6092
-recovered Augustus_model.g41146.t1, internal, 6419, 6476
Couldn't classify 248, 294
Sorry, prediction snap_scaffold_479-snap.2-T1 fails validation.
(AAC)	 AG	248-294	GT	TGG
(GTA)	 AG	790-971	GT	TGG
(GGT)	 AG	2918-3208	GT	GGG
(TGC)	 AG	5108-5539	AC	GAA
-recovered snap_scaffold_479-snap.2-T1, terminal, 5108, 5539
-recovered snap_scaffold_479-snap.2-T1, internal, 248, 294
-recovered snap_scaffold_479-snap.2-T1, internal, 790, 971
-recovered snap_scaffold_479-snap.2-T1, internal, 2918, 3208
Valid prediction for GeneMark_model.107748_t
Couldn't classify 6419, 6476
Sorry, prediction snap_scaffold_479-snap.1-T1 fails validation.
(ATG)	 AC	5542-5579	GT	GGG
(GTG)	 AG	5990-6092	GT	ATG
(GCA)	 AG	6419-6476	GT	TGG
-recovered snap_scaffold_479-snap.1-T1, initial, 5542, 5579
-recovered snap_scaffold_479-snap.1-T1, internal, 5990, 6092
-recovered snap_scaffold_479-snap.1-T1, internal, 6419, 6476

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6395, rend_intergenic: 1613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 6642
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 6395, rend_intergenic: 1613  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