-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_119

-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 591, 677
Couldn't classify 10969, 11176
Sorry, prediction snap_scaffold_119-snap.1-T1 fails validation.
(GGG)	 AG	591-677	GT	AGG
(CCA)	 AG	1742-1995	GT	GGG
(GCA)	 AG	3794-3899	GT	GGG
(GCA)	 AG	4518-4623	GT	GGG
(ACG)	 AG	5154-5308	GT	ACG
(CGG)	 AG	5337-5464	GT	CGG
(GGT)	 AG	8967-9032	GT	AAG
(AAC)	 AG	10969-11176	GT	AAG
-recovered snap_scaffold_119-snap.1-T1, internal, 591, 677
-recovered snap_scaffold_119-snap.1-T1, internal, 1742, 1995
-recovered snap_scaffold_119-snap.1-T1, internal, 3794, 3899
-recovered snap_scaffold_119-snap.1-T1, internal, 4518, 4623
-recovered snap_scaffold_119-snap.1-T1, internal, 5154, 5308
-recovered snap_scaffold_119-snap.1-T1, internal, 5337, 5464
-recovered snap_scaffold_119-snap.1-T1, internal, 8967, 9032
-recovered snap_scaffold_119-snap.1-T1, internal, 10969, 11176
Valid prediction for GeneMark_model.106636_t
Valid prediction for GlimmerHMM_glimmerT_61328-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61328-T1 1742-2001-terminal-1 is invalid.
Couldn't classify 1742, 1935
Sorry, prediction Augustus_model.g40795.t1 fails validation.
(CCA)	 AG	1742-1935	GT	AGG
(TTG)	 AG	2476-2625	AC	AAA
-recovered Augustus_model.g40795.t1, terminal, 2476, 2625
-recovered Augustus_model.g40795.t1, internal, 1742, 1935

-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 GeneMark_model.106637_t
Valid prediction for GeneMark_model.106635_t
Couldn't classify 5649, 5775
Sorry, prediction GlimmerHMM_glimmerT_61330-T1 fails validation.
(CGC)	 AG	5649-5775	GT	CCG
(AGC)	 AG	9874-10095	CG	GAC
-recovered GlimmerHMM_glimmerT_61330-T1, terminal, 9874, 10095
-recovered GlimmerHMM_glimmerT_61330-T1, internal, 5649, 5775
Couldn't classify 3352, 3589
Sorry, prediction snap_scaffold_119-snap.3-T1 fails validation.
(CAG)	 AG	3352-3589	GT	GTG
(CCT)	 AG	5446-5775	GT	CCG
(CTA)	 AG	7157-7216	AT	AGA
-recovered snap_scaffold_119-snap.3-T1, terminal, 7157, 7216
-recovered snap_scaffold_119-snap.3-T1, internal, 3352, 3589
-recovered snap_scaffold_119-snap.3-T1, internal, 5446, 5775
Couldn't classify 14024, 14205
Sorry, prediction GeneMark_model.106634_t fails validation.
(ATG)	 GC	13785-13922	GT	TGG
(CCT)	 AG	14024-14205	GT	ATG
-recovered GeneMark_model.106634_t, initial, 13785, 13922
-recovered GeneMark_model.106634_t, internal, 14024, 14205
Valid prediction for snap_scaffold_119-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_61329-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11176, rend_intergenic: 1161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 14487
-exon list size: 66


building trellis

1.5    
2.9    
4.4    
5.9    
7.4    
8.8    
10.3    
11.8    
13.2    
14.7    
16.2    
17.6    
19.1    
20.6    
22.1    
23.5    
25.0    
26.5    
27.9    
29.4    
30.9    
32.4    
33.8    
35.3    
36.8    
38.2    
39.7    
41.2    
42.6    
44.1    
45.6    
47.1    
48.5    
50.0    
51.5    
52.9    
54.4    
55.9    
57.4    
58.8    
60.3    
61.8    
63.2    
64.7    
66.2    
67.6    
69.1    
70.6    
72.1    
73.5    
75.0    
76.5    
77.9    
79.4    
80.9    
82.4    
83.8    
85.3    
86.8    
88.2    
89.7    
91.2    
92.6    
94.1    
95.6    
97.1    
98.5    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 11176, rend_intergenic: 1161  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