-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_233

-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 6697, 6886
Sorry, prediction snap_scaffold_233-snap.2-T1 fails validation.
(ATG)	 GC	977-991	GT	GAG
(GCT)	 AG	5927-6005	GT	AGG
(AGA)	 AG	6697-6886	GT	AGG
-recovered snap_scaffold_233-snap.2-T1, initial, 977, 991
-recovered snap_scaffold_233-snap.2-T1, internal, 5927, 6005
-recovered snap_scaffold_233-snap.2-T1, internal, 6697, 6886
Valid prediction for GeneMark_model.107015_t
Couldn't classify 7657, 7798
Sorry, prediction GeneMark_model.107017_t fails validation.
(ATG)	 CT	6668-6690	GT	GAG
(TGA)	 AG	6751-6771	GT	AGG
(GGA)	 AG	6809-6886	GT	AGG
(GAA)	 AG	6975-6992	GT	AGG
(GAC)	 AG	7036-7044	GT	AAG
(GAA)	 AG	7388-7399	GT	GAG
(GGG)	 AG	7443-7448	GT	GAG
(GGG)	 AG	7546-7557	GT	GGG
(GGG)	 AG	7614-7631	GT	GGG
(CCA)	 AG	7657-7798	GT	GAG
-recovered GeneMark_model.107017_t, initial, 6668, 6690
-recovered GeneMark_model.107017_t, terminal, 7388, 7399
-recovered GeneMark_model.107017_t, internal, 6751, 6771
-recovered GeneMark_model.107017_t, internal, 6809, 6886
-recovered GeneMark_model.107017_t, internal, 6975, 6992
-recovered GeneMark_model.107017_t, internal, 7036, 7044
-recovered GeneMark_model.107017_t, internal, 7388, 7399
-recovered GeneMark_model.107017_t, internal, 7443, 7448
-recovered GeneMark_model.107017_t, internal, 7546, 7557
-recovered GeneMark_model.107017_t, internal, 7614, 7631
-recovered GeneMark_model.107017_t, internal, 7657, 7798
Couldn't classify 149, 357
Sorry, prediction GeneMark_model.107013_t fails validation.
(CTT)	 AG	149-357	GT	GGG
(ACA)	 AG	681-692	GT	GGG
(AAG)	 AG	721-1006	AA	AGA
-recovered GeneMark_model.107013_t, terminal, 721, 1006
-recovered GeneMark_model.107013_t, internal, 149, 357
-recovered GeneMark_model.107013_t, internal, 681, 692

-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 8988, 9145
Sorry, prediction snap_scaffold_233-snap.1-T1 fails validation.
(ATG)	 AC	4609-4653	GT	TGG
(GGG)	 AG	8988-9145	GT	CAG
-recovered snap_scaffold_233-snap.1-T1, initial, 4609, 4653
-recovered snap_scaffold_233-snap.1-T1, internal, 8988, 9145
Valid prediction for GlimmerHMM_glimmerT_61546-T1
Valid prediction for GeneMark_model.107014_t
Couldn't classify 2454, 2500
Sorry, prediction snap_scaffold_233-snap.3-T1 fails validation.
(GGC)	 AG	2454-2500	GT	TGG
(GAC)	 AG	2512-2523	GT	AGG
(CAC)	 AG	3201-3483	GT	CGG
(GAG)	 AG	4139-4161	GG	AGG
-recovered snap_scaffold_233-snap.3-T1, terminal, 4139, 4161
-recovered snap_scaffold_233-snap.3-T1, internal, 2454, 2500
-recovered snap_scaffold_233-snap.3-T1, internal, 2512, 2523
-recovered snap_scaffold_233-snap.3-T1, internal, 3201, 3483

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4677, rend_intergenic: 977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6886, rend_intergenic: 5125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 9285
-exon list size: 53


building trellis

1.8    
3.6    
5.5    
7.3    
9.1    
10.9    
12.7    
14.5    
16.4    
18.2    
20.0    
21.8    
23.6    
25.5    
27.3    
29.1    
30.9    
32.7    
34.5    
36.4    
38.2    
40.0    
41.8    
43.6    
45.5    
47.3    
49.1    
50.9    
52.7    
54.5    
56.4    
58.2    
60.0    
61.8    
63.6    
65.5    
67.3    
69.1    
70.9    
72.7    
74.5    
76.4    
78.2    
80.0    
81.8    
83.6    
85.5    
87.3    
89.1    
90.9    
92.7    
94.5    
96.4    
98.2    
-found 4 predictions from path traversal
Error with prediction: snap lend_intergenic: 4677, rend_intergenic: 977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6886, rend_intergenic: 5125  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