-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_835

-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 553, 1042
Sorry, prediction snap_scaffold_835-snap.2-T1 fails validation.
(GAG)	 AG	553-1042	GT	GAG
(GTA)	 AG	2577-2688	GT	AGG
(GCC)	 AG	3377-3678	TT	GAT
add_exon() Sorry, snap_scaffold_835-snap.2-T1 2577-2688-terminal-3 is invalid.
-recovered snap_scaffold_835-snap.2-T1, terminal, 2577, 2688
-recovered snap_scaffold_835-snap.2-T1, terminal, 3377, 3678
-recovered snap_scaffold_835-snap.2-T1, internal, 553, 1042
-recovered snap_scaffold_835-snap.2-T1, internal, 2577, 2688
Valid prediction for GeneMark_model.108458_t
Valid prediction for GeneMark_model.108457_t

-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 162, 374
Couldn't classify 4048, 4243
Sorry, prediction Augustus_model.g41396.t1 fails validation.
(GTC)	 AG	162-374	GT	CGG
(CAA)	 AG	543-776	GT	TGG
(TCC)	 AG	1563-1724	GT	AGG
(CGC)	 AG	1847-2008	GT	AGG
(GAC)	 AG	2488-2634	GT	CAG
(GTT)	 AG	3723-3811	GT	AGG
(GTG)	 AG	4048-4243	GT	TGG
-recovered Augustus_model.g41396.t1, internal, 162, 374
-recovered Augustus_model.g41396.t1, internal, 543, 776
-recovered Augustus_model.g41396.t1, internal, 1563, 1724
-recovered Augustus_model.g41396.t1, internal, 1847, 2008
-recovered Augustus_model.g41396.t1, internal, 2488, 2634
-recovered Augustus_model.g41396.t1, internal, 3723, 3811
-recovered Augustus_model.g41396.t1, internal, 4048, 4243
Couldn't classify 162, 374
Couldn't classify 4145, 4243
Sorry, prediction snap_scaffold_835-snap.1-T1 fails validation.
(GTC)	 AG	162-374	GT	CGG
(CAA)	 AG	543-776	GT	TGG
(TCC)	 AG	1563-1724	GT	AGG
(CGC)	 AG	1847-2008	GT	AGG
(GAC)	 AG	2488-2634	GT	CAG
(GTT)	 AG	3723-3822	GT	ATG
(GTG)	 AG	4048-4112	GT	GGG
(GTA)	 AG	4145-4243	GT	TGG
-recovered snap_scaffold_835-snap.1-T1, internal, 162, 374
-recovered snap_scaffold_835-snap.1-T1, internal, 543, 776
-recovered snap_scaffold_835-snap.1-T1, internal, 1563, 1724
-recovered snap_scaffold_835-snap.1-T1, internal, 1847, 2008
-recovered snap_scaffold_835-snap.1-T1, internal, 2488, 2634
-recovered snap_scaffold_835-snap.1-T1, internal, 3723, 3822
-recovered snap_scaffold_835-snap.1-T1, internal, 4048, 4112
-recovered snap_scaffold_835-snap.1-T1, internal, 4145, 4243
Couldn't classify 12, 45
Sorry, prediction GeneMark_model.108459_t fails validation.
(TAC)	 AG	12-45	GT	TGG
(GTC)	 AG	162-374	GT	CGG
(CAA)	 AG	543-780	GT	GAG
(CAG)	 AG	1255-1400	GT	GGG
(TCC)	 AG	1563-1724	GT	AGG
(CGC)	 AG	1847-2151	AT	AGA
-recovered GeneMark_model.108459_t, terminal, 543, 780
-recovered GeneMark_model.108459_t, terminal, 1847, 2151
-recovered GeneMark_model.108459_t, internal, 12, 45
-recovered GeneMark_model.108459_t, internal, 162, 374
-recovered GeneMark_model.108459_t, internal, 543, 780
-recovered GeneMark_model.108459_t, internal, 1255, 1400
-recovered GeneMark_model.108459_t, internal, 1563, 1724
Couldn't classify 162, 374
Sorry, prediction GlimmerHMM_glimmerT_62280-T1 fails validation.
(GTC)	 AG	162-374	GT	CGG
(CAA)	 AG	543-776	GT	TGG
(TCC)	 AG	1563-1724	GT	AGG
(CGC)	 AG	1847-2008	GT	AGG
(GAC)	 AG	2488-2638	GT	GGG
(GTT)	 AG	3723-3774	GG	GAG
-recovered GlimmerHMM_glimmerT_62280-T1, terminal, 3723, 3774
-recovered GlimmerHMM_glimmerT_62280-T1, internal, 162, 374
-recovered GlimmerHMM_glimmerT_62280-T1, internal, 543, 776
-recovered GlimmerHMM_glimmerT_62280-T1, internal, 1563, 1724
-recovered GlimmerHMM_glimmerT_62280-T1, internal, 1847, 2008
-recovered GlimmerHMM_glimmerT_62280-T1, internal, 2488, 2638

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4108, rend_intergenic: 553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 4269
-exon list size: 40


building trellis

2.4    
4.8    
7.1    
9.5    
11.9    
14.3    
16.7    
19.0    
21.4    
23.8    
26.2    
28.6    
31.0    
33.3    
35.7    
38.1    
40.5    
42.9    
45.2    
47.6    
50.0    
52.4    
54.8    
57.1    
59.5    
61.9    
64.3    
66.7    
69.0    
71.4    
73.8    
76.2    
78.6    
81.0    
83.3    
85.7    
88.1    
90.5    
92.9    
95.2    
97.6    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 4108, rend_intergenic: 553  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