-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_650

-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 5099, 5143
Sorry, prediction GeneMark_model.108131_t fails validation.
(ATG)	 CA	2042-2158	GT	GGG
(GAG)	 AG	3519-3559	GT	AGG
(AGA)	 AG	3588-3866	GT	GAG
(GAG)	 AG	3892-3903	GT	ACG
(CGC)	 AG	4035-4127	GT	GGG
(GGG)	 AG	4928-5074	GT	GAG
(GAA)	 AG	5099-5143	GT	GGG
-recovered GeneMark_model.108131_t, initial, 2042, 2158
-recovered GeneMark_model.108131_t, internal, 3519, 3559
-recovered GeneMark_model.108131_t, internal, 3588, 3866
-recovered GeneMark_model.108131_t, internal, 3892, 3903
-recovered GeneMark_model.108131_t, internal, 4035, 4127
-recovered GeneMark_model.108131_t, internal, 4928, 5074
-recovered GeneMark_model.108131_t, internal, 5099, 5143
Couldn't classify 166, 264
Sorry, prediction snap_scaffold_650-snap.2-T1 fails validation.
(GGT)	 AG	166-264	GT	CCG
(GAG)	 AG	3519-3870	AA	GAA
-recovered snap_scaffold_650-snap.2-T1, terminal, 3519, 3870
-recovered snap_scaffold_650-snap.2-T1, internal, 166, 264
Valid prediction for GlimmerHMM_glimmerT_62085-T1
Valid prediction for Augustus_model.g41271.t1
Couldn't classify 4805, 5143
Sorry, prediction snap_scaffold_650-snap.3-T1 fails validation.
(ATG)	 TC	4045-4127	GT	GGG
(CTG)	 AG	4805-5143	GT	GGG
-recovered snap_scaffold_650-snap.3-T1, initial, 4045, 4127
-recovered snap_scaffold_650-snap.3-T1, internal, 4805, 5143

-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 4882, 5007
Sorry, prediction snap_scaffold_650-snap.1-T1 fails validation.
(ATG)	 AG	1628-1822	GT	GTG
(AAT)	 AG	1857-1892	GT	AGG
(GAG)	 AG	4480-4691	GT	AGG
(GAG)	 AG	4882-5007	GT	CAG
-recovered snap_scaffold_650-snap.1-T1, initial, 1628, 1822
add_exon() Sorry, snap_scaffold_650-snap.1-T1 4480-4691-terminal-2 is invalid.
-recovered snap_scaffold_650-snap.1-T1, terminal, 4480, 4691
-recovered snap_scaffold_650-snap.1-T1, internal, 1628, 1822
-recovered snap_scaffold_650-snap.1-T1, internal, 1857, 1892
-recovered snap_scaffold_650-snap.1-T1, internal, 4480, 4691
-recovered snap_scaffold_650-snap.1-T1, internal, 4882, 5007
Couldn't classify 5045, 5141
Sorry, prediction GeneMark_model.108130_t fails validation.
(ATG)	 TG	3505-3511	GT	GGG
(AGG)	 AG	3537-3546	GT	GAG
(AAG)	 AG	3586-3718	GT	GAG
(ATA)	 AG	3938-3971	GT	TGG
(GAG)	 AG	4076-4091	GT	GAG
(GAA)	 AG	4288-4374	GT	ACG
(GAG)	 AG	4413-4430	GT	GAG
(GAG)	 AG	4480-4503	GT	GAG
(GGG)	 AG	4526-4552	GT	AGG
(GGG)	 AG	4590-4691	GT	AGG
(ACA)	 AG	4885-5007	GT	CAG
(AGA)	 AG	5045-5141	GT	GGG
-recovered GeneMark_model.108130_t, initial, 3505, 3511
-recovered GeneMark_model.108130_t, terminal, 4076, 4091
-recovered GeneMark_model.108130_t, terminal, 4590, 4691
-recovered GeneMark_model.108130_t, internal, 3537, 3546
-recovered GeneMark_model.108130_t, internal, 3586, 3718
-recovered GeneMark_model.108130_t, internal, 3938, 3971
-recovered GeneMark_model.108130_t, internal, 4076, 4091
-recovered GeneMark_model.108130_t, internal, 4288, 4374
-recovered GeneMark_model.108130_t, internal, 4413, 4430
-recovered GeneMark_model.108130_t, internal, 4480, 4503
-recovered GeneMark_model.108130_t, internal, 4526, 4552
-recovered GeneMark_model.108130_t, internal, 4590, 4691
-recovered GeneMark_model.108130_t, internal, 4885, 5007
-recovered GeneMark_model.108130_t, internal, 5045, 5141

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3525, rend_intergenic: 166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 5152
-exon list size: 57


building trellis

1.7    
3.4    
5.1    
6.8    
8.5    
10.2    
11.9    
13.6    
15.3    
16.9    
18.6    
20.3    
22.0    
23.7    
25.4    
27.1    
28.8    
30.5    
32.2    
33.9    
35.6    
37.3    
39.0    
40.7    
42.4    
44.1    
45.8    
47.5    
49.2    
50.8    
52.5    
54.2    
55.9    
57.6    
59.3    
61.0    
62.7    
64.4    
66.1    
67.8    
69.5    
71.2    
72.9    
74.6    
76.3    
78.0    
79.7    
81.4    
83.1    
84.7    
86.4    
88.1    
89.8    
91.5    
93.2    
94.9    
96.6    
98.3    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 3525, 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 1 predictions persist after filtering for low support