-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/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

-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, 371
Sorry, prediction GlimmerHMM_glimmerT_60725-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	4271-4374	AG	GAA
add_exon() Sorry, GlimmerHMM_glimmerT_60725-T1 2921-3028-terminal-1 is invalid.
-recovered GlimmerHMM_glimmerT_60725-T1, terminal, 2921, 3028
-recovered GlimmerHMM_glimmerT_60725-T1, terminal, 4271, 4374
-recovered GlimmerHMM_glimmerT_60725-T1, internal, 95, 371
-recovered GlimmerHMM_glimmerT_60725-T1, internal, 719, 916
-recovered GlimmerHMM_glimmerT_60725-T1, internal, 1730, 1827
-recovered GlimmerHMM_glimmerT_60725-T1, internal, 2620, 2710
-recovered GlimmerHMM_glimmerT_60725-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.g40197.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.g40197.t1 2921-3028-terminal-1 is invalid.
-recovered Augustus_model.g40197.t1, terminal, 2921, 3028
-recovered Augustus_model.g40197.t1, internal, 95, 371
-recovered Augustus_model.g40197.t1, internal, 719, 923
-recovered Augustus_model.g40197.t1, internal, 1415, 1509
-recovered Augustus_model.g40197.t1, internal, 1730, 1827
-recovered Augustus_model.g40197.t1, internal, 2620, 2710
-recovered Augustus_model.g40197.t1, internal, 2921, 3028
-recovered Augustus_model.g40197.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: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-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