-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_162

-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 366, 467
Sorry, prediction snap_scaffold_162-snap.2-T1 fails validation.
(GGT)	 AG	366-467	GT	AGG
(GAG)	 AG	761-880	GT	AGG
(ATG)	 AG	3730-3828	GT	AGG
(CTG)	 AG	4372-4524	GT	TGG
(AGC)	 AG	6363-6451	GT	AGG
(GCT)	 AG	9572-10136	GG	GAG
-recovered snap_scaffold_162-snap.2-T1, initial, 3730, 3828
-recovered snap_scaffold_162-snap.2-T1, terminal, 9572, 10136
-recovered snap_scaffold_162-snap.2-T1, internal, 366, 467
-recovered snap_scaffold_162-snap.2-T1, internal, 761, 880
-recovered snap_scaffold_162-snap.2-T1, internal, 3730, 3828
-recovered snap_scaffold_162-snap.2-T1, internal, 4372, 4524
-recovered snap_scaffold_162-snap.2-T1, internal, 6363, 6451
Valid prediction for GeneMark_model.106792_t
Couldn't classify 11393, 11644
Sorry, prediction GeneMark_model.106795_t fails validation.
(ATG)	 GG	11167-11231	GT	AGG
(ACC)	 AG	11393-11644	GT	AGG
-recovered GeneMark_model.106795_t, initial, 11167, 11231
-recovered GeneMark_model.106795_t, internal, 11393, 11644
Couldn't classify 11331, 11644
Sorry, prediction snap_scaffold_162-snap.4-T1 fails validation.
(ATG)	 GG	10253-10528	GT	AGG
(TAT)	 AG	11331-11644	GT	AGG
-recovered snap_scaffold_162-snap.4-T1, initial, 10253, 10528
-recovered snap_scaffold_162-snap.4-T1, internal, 11331, 11644
Valid prediction for GlimmerHMM_glimmerT_61427-T1
Couldn't classify 366, 467
Sorry, prediction Augustus_model.g40852.t1 fails validation.
(GGT)	 AG	366-467	GT	AGG
(GAG)	 AG	761-880	GT	AGG
(ATG)	 AG	3730-3828	GT	AGG
(CTG)	 AG	4372-4524	GT	TGG
(AGC)	 AG	6363-6451	GT	AGG
(CCT)	 AG	8191-8280	GT	AAG
(TGA)	 AG	10598-10642	GT	AGG
(CAC)	 AG	11378-11648	GG	GAG
-recovered Augustus_model.g40852.t1, initial, 3730, 3828
-recovered Augustus_model.g40852.t1, terminal, 11378, 11648
-recovered Augustus_model.g40852.t1, internal, 366, 467
-recovered Augustus_model.g40852.t1, internal, 761, 880
-recovered Augustus_model.g40852.t1, internal, 3730, 3828
-recovered Augustus_model.g40852.t1, internal, 4372, 4524
-recovered Augustus_model.g40852.t1, internal, 6363, 6451
-recovered Augustus_model.g40852.t1, internal, 8191, 8280
-recovered Augustus_model.g40852.t1, internal, 10598, 10642
Couldn't classify 3736, 3828
Couldn't classify 4372, 4605
Sorry, prediction pasa_asmbl_17637.p1 fails validation.
(TAC)	 GG	3736-3828	GT	AGG
(CTG)	 AG	4372-4605	TG	GGT

-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 GlimmerHMM_glimmerT_61428-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61428-T1 103-356-initial-1 is invalid.
Couldn't classify 11682, 11691
Sorry, prediction GeneMark_model.106791_t fails validation.
(ATG)	 AG	11317-11654	GT	GGG
(GGA)	 AG	11682-11691	GC	TGG
-recovered GeneMark_model.106791_t, initial, 11317, 11654
-recovered GeneMark_model.106791_t, internal, 11317, 11654
-recovered GeneMark_model.106791_t, internal, 11682, 11691
Valid prediction for GeneMark_model.106794_t
Valid prediction for GeneMark_model.106793_t
Valid prediction for snap_scaffold_162-snap.3-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 11355, 11686
Sorry, prediction snap_scaffold_162-snap.1-T1 fails validation.
(ATG)	 AC	6327-6958	GT	AGG
(TCT)	 AG	7210-7367	GT	AAG
(TTC)	 AG	10821-10905	GT	ATG
(GAG)	 AG	11355-11686	GT	GGG
-recovered snap_scaffold_162-snap.1-T1, initial, 6327, 6958
add_exon() Sorry, snap_scaffold_162-snap.1-T1 7210-7367-terminal-2 is invalid.
-recovered snap_scaffold_162-snap.1-T1, terminal, 7210, 7367
-recovered snap_scaffold_162-snap.1-T1, internal, 7210, 7367
-recovered snap_scaffold_162-snap.1-T1, internal, 10821, 10905
-recovered snap_scaffold_162-snap.1-T1, internal, 11355, 11686

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5387, rend_intergenic: 366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10136, rend_intergenic: 5447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 11713
-exon list size: 71


building trellis

1.4    
2.7    
4.1    
5.5    
6.8    
8.2    
9.6    
11.0    
12.3    
13.7    
15.1    
16.4    
17.8    
19.2    
20.5    
21.9    
23.3    
24.7    
26.0    
27.4    
28.8    
30.1    
31.5    
32.9    
34.2    
35.6    
37.0    
38.4    
39.7    
41.1    
42.5    
43.8    
45.2    
46.6    
47.9    
49.3    
50.7    
52.1    
53.4    
54.8    
56.2    
57.5    
58.9    
60.3    
61.6    
63.0    
64.4    
65.8    
67.1    
68.5    
69.9    
71.2    
72.6    
74.0    
75.3    
76.7    
78.1    
79.5    
80.8    
82.2    
83.6    
84.9    
86.3    
87.7    
89.0    
90.4    
91.8    
93.2    
94.5    
95.9    
97.3    
98.6    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 5387, rend_intergenic: 366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10136, rend_intergenic: 5447  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