-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_499

-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.107806_t
Couldn't classify 166, 252
Sorry, prediction snap_scaffold_499-snap.2-T1 fails validation.
(GGG)	 AG	166-252	GT	CGG
(GTG)	 AG	950-1025	GT	CGG
(GGC)	 AG	1707-1836	GG	GAG
-recovered snap_scaffold_499-snap.2-T1, terminal, 1707, 1836
-recovered snap_scaffold_499-snap.2-T1, internal, 166, 252
-recovered snap_scaffold_499-snap.2-T1, internal, 950, 1025
Valid prediction for GeneMark_model.107805_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: -)Valid prediction for snap_scaffold_499-snap.1-T1
Valid prediction for snap_scaffold_499-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_61924-T1
Couldn't classify 6162, 6315
Sorry, prediction GeneMark_model.107803_t fails validation.
(ATG)	 GT	5728-5821	GT	CTG
(TCA)	 AG	5951-6078	GT	TAG
(GCA)	 AG	6162-6315	GT	TGG
-recovered GeneMark_model.107803_t, initial, 5728, 5821
-recovered GeneMark_model.107803_t, internal, 5951, 6078
-recovered GeneMark_model.107803_t, internal, 6162, 6315
Couldn't classify 518, 524
Sorry, prediction GeneMark_model.107807_t fails validation.
(AGA)	 AG	518-524	GT	AGG
(GTG)	 AG	641-689	GT	AGG
(ACC)	 AG	720-777	GC	GGG
(GGG)	 AG	816-848	GT	AGG
(AGA)	 AG	897-968	GT	ATG
(AGA)	 AG	1018-1023	GT	AGG
(AGA)	 AG	1048-1150	AA	GAA
-recovered GeneMark_model.107807_t, terminal, 1048, 1150
-recovered GeneMark_model.107807_t, internal, 518, 524
-recovered GeneMark_model.107807_t, internal, 641, 689
-recovered GeneMark_model.107807_t, internal, 720, 777
-recovered GeneMark_model.107807_t, internal, 816, 848
-recovered GeneMark_model.107807_t, internal, 897, 968
-recovered GeneMark_model.107807_t, internal, 1018, 1023
Couldn't classify 641, 689
Sorry, prediction Augustus_model.g41162.t1 fails validation.
(GTG)	 AG	641-689	GT	AGG
(CTC)	 AG	1433-1482	GT	GGG
(CTA)	 AG	1639-1850	GT	AGG
(TCA)	 AG	2355-2546	GT	GGG
(TGC)	 AG	3413-3614	CA	AAC
-recovered Augustus_model.g41162.t1, terminal, 3413, 3614
-recovered Augustus_model.g41162.t1, internal, 641, 689
-recovered Augustus_model.g41162.t1, internal, 1433, 1482
-recovered Augustus_model.g41162.t1, internal, 1639, 1850
-recovered Augustus_model.g41162.t1, internal, 2355, 2546
Valid prediction for GlimmerHMM_glimmerT_61926-T1
Valid prediction for GeneMark_model.107804_t
Valid prediction for snap_scaffold_499-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_61925-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 1642, rend_intergenic: 166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 6447
-exon list size: 59


building trellis

1.6    
3.3    
4.9    
6.6    
8.2    
9.8    
11.5    
13.1    
14.8    
16.4    
18.0    
19.7    
21.3    
23.0    
24.6    
26.2    
27.9    
29.5    
31.1    
32.8    
34.4    
36.1    
37.7    
39.3    
41.0    
42.6    
44.3    
45.9    
47.5    
49.2    
50.8    
52.5    
54.1    
55.7    
57.4    
59.0    
60.7    
62.3    
63.9    
65.6    
67.2    
68.9    
70.5    
72.1    
73.8    
75.4    
77.0    
78.7    
80.3    
82.0    
83.6    
85.2    
86.9    
88.5    
90.2    
91.8    
93.4    
95.1    
96.7    
98.4    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 1642, rend_intergenic: 166  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