-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_778

-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 149, 400
Sorry, prediction snap_scaffold_778-snap.2-T1 fails validation.
(GAG)	 AG	149-400	GT	AGG
(TGA)	 AG	2698-2791	GT	ATG
(CGA)	 AG	3010-3220	GT	AAG
(GTG)	 AG	3632-3682	GT	GCG
(CCA)	 AG	3742-4082	GT	CCG
(TCC)	 AG	4289-4471	GG	GAG
-recovered snap_scaffold_778-snap.2-T1, terminal, 4289, 4471
-recovered snap_scaffold_778-snap.2-T1, internal, 149, 400
-recovered snap_scaffold_778-snap.2-T1, internal, 2698, 2791
-recovered snap_scaffold_778-snap.2-T1, internal, 3010, 3220
-recovered snap_scaffold_778-snap.2-T1, internal, 3632, 3682
-recovered snap_scaffold_778-snap.2-T1, internal, 3742, 4082
Valid prediction for GeneMark_model.108364_t
Couldn't classify 43, 66
Sorry, prediction GeneMark_model.108363_t fails validation.
(AGA)	 AG	43-66	GT	GAG
(GGA)	 AG	90-101	GT	GGG
(GAG)	 AG	268-345	GT	AAG
(GAA)	 AG	369-419	GT	GGG
(GGA)	 AG	449-518	GG	GAG
-recovered GeneMark_model.108363_t, terminal, 43, 66
-recovered GeneMark_model.108363_t, terminal, 449, 518
-recovered GeneMark_model.108363_t, internal, 43, 66
-recovered GeneMark_model.108363_t, internal, 90, 101
-recovered GeneMark_model.108363_t, internal, 268, 345
-recovered GeneMark_model.108363_t, internal, 369, 419

-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 95, 198
Sorry, prediction GeneMark_model.108365_t fails validation.
(TAC)	 AG	95-198	GT	GTG
(GGA)	 AG	250-400	AT	AGA
-recovered GeneMark_model.108365_t, terminal, 250, 400
-recovered GeneMark_model.108365_t, internal, 95, 198
Couldn't classify 95, 371
Sorry, prediction GlimmerHMM_glimmerT_62224-T1 fails validation.
(TAC)	 AG	95-371	GT	CTG
(TGT)	 AG	719-923	GT	AGG
(AGC)	 AG	1394-1509	GT	AGG
(TGG)	 AG	1730-1807	GT	CAG
(GCT)	 AG	2921-3028	GT	AGG
(AGA)	 AG	4271-4374	AG	GAA
add_exon() Sorry, GlimmerHMM_glimmerT_62224-T1 2921-3028-terminal-1 is invalid.
-recovered GlimmerHMM_glimmerT_62224-T1, terminal, 2921, 3028
-recovered GlimmerHMM_glimmerT_62224-T1, terminal, 4271, 4374
-recovered GlimmerHMM_glimmerT_62224-T1, internal, 95, 371
-recovered GlimmerHMM_glimmerT_62224-T1, internal, 719, 923
-recovered GlimmerHMM_glimmerT_62224-T1, internal, 1394, 1509
-recovered GlimmerHMM_glimmerT_62224-T1, internal, 1730, 1807
-recovered GlimmerHMM_glimmerT_62224-T1, internal, 2921, 3028
Couldn't classify 95, 371
Couldn't classify 4271, 4370
Sorry, prediction snap_scaffold_778-snap.1-T1 fails validation.
(TAC)	 AG	95-371	GT	CTG
(TGT)	 AG	719-916	GT	AGG
(TGG)	 AG	1730-1827	GT	CCG
(GGA)	 AG	2620-2710	GT	CAG
(GCT)	 AG	2921-3028	GT	AGG
(AGA)	 AG	4271-4370	GT	AGG
add_exon() Sorry, snap_scaffold_778-snap.1-T1 2921-3028-terminal-1 is invalid.
-recovered snap_scaffold_778-snap.1-T1, terminal, 2921, 3028
-recovered snap_scaffold_778-snap.1-T1, internal, 95, 371
-recovered snap_scaffold_778-snap.1-T1, internal, 719, 916
-recovered snap_scaffold_778-snap.1-T1, internal, 1730, 1827
-recovered snap_scaffold_778-snap.1-T1, internal, 2620, 2710
-recovered snap_scaffold_778-snap.1-T1, internal, 2921, 3028
-recovered snap_scaffold_778-snap.1-T1, internal, 4271, 4370
Couldn't classify 95, 371
Couldn't classify 4271, 4370
Sorry, prediction Augustus_model.g41363.t1 fails validation.
(TAC)	 AG	95-371	GT	CTG
(TGT)	 AG	719-923	GT	AGG
(ATT)	 AG	1415-1509	GT	AGG
(TGG)	 AG	1730-1827	GT	CCG
(GGA)	 AG	2620-2710	GT	CAG
(GCT)	 AG	2921-3028	GT	AGG
(AGA)	 AG	4271-4370	GT	AGG
add_exon() Sorry, Augustus_model.g41363.t1 2921-3028-terminal-1 is invalid.
-recovered Augustus_model.g41363.t1, terminal, 2921, 3028
-recovered Augustus_model.g41363.t1, internal, 95, 371
-recovered Augustus_model.g41363.t1, internal, 719, 923
-recovered Augustus_model.g41363.t1, internal, 1415, 1509
-recovered Augustus_model.g41363.t1, internal, 1730, 1827
-recovered Augustus_model.g41363.t1, internal, 2620, 2710
-recovered Augustus_model.g41363.t1, internal, 2921, 3028
-recovered Augustus_model.g41363.t1, internal, 4271, 4370

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4416, rend_intergenic: 149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 4510
-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 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 4416, rend_intergenic: 149  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