-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_890

-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: +)Valid prediction for snap_scaffold_890-snap.3-T1
Couldn't classify 148, 295
Sorry, prediction Augustus_model.g41422.t1 fails validation.
(CTC)	 AG	148-295	GT	AGG
(GGC)	 AG	534-668	GT	TGG
(CTT)	 AG	766-815	GT	GGG
(TTC)	 AG	923-1305	GT	AGG
(TTA)	 AG	2036-2096	AG	AGA
-recovered Augustus_model.g41422.t1, terminal, 2036, 2096
-recovered Augustus_model.g41422.t1, internal, 148, 295
-recovered Augustus_model.g41422.t1, internal, 534, 668
-recovered Augustus_model.g41422.t1, internal, 766, 815
-recovered Augustus_model.g41422.t1, internal, 923, 1305
Couldn't classify 156, 295
Sorry, prediction snap_scaffold_890-snap.1-T1 fails validation.
(ATC)	 AG	156-295	GT	AGG
(GGC)	 AG	534-668	GT	TGG
(CTT)	 AG	766-815	GT	GGG
(TTC)	 AG	923-1305	GT	AGG
(AGG)	 AG	2223-2355	AG	AAA
-recovered snap_scaffold_890-snap.1-T1, terminal, 2223, 2355
-recovered snap_scaffold_890-snap.1-T1, internal, 156, 295
-recovered snap_scaffold_890-snap.1-T1, internal, 534, 668
-recovered snap_scaffold_890-snap.1-T1, internal, 766, 815
-recovered snap_scaffold_890-snap.1-T1, internal, 923, 1305
Valid prediction for GlimmerHMM_glimmerT_62318-T1
Couldn't classify 148, 295
Sorry, prediction GeneMark_model.108555_t fails validation.
(CTC)	 AG	148-295	GT	AGG
(GGC)	 AG	534-668	GT	TGG
(CTT)	 AG	766-815	GT	GGG
(TTC)	 AG	923-1305	GT	AGG
(GGG)	 AG	1334-1381	GT	ATG
(TCT)	 AG	2201-2266	GT	GAG
(GGA)	 AG	2506-2769	GC	AGG
(ACA)	 AG	2790-2825	GC	AGG
(ACA)	 AG	2850-2897	GT	GAG
(GAA)	 AG	3013-3114	GT	GAG
(GAG)	 AG	3545-3662	CA	GAC
-recovered GeneMark_model.108555_t, terminal, 3545, 3662
-recovered GeneMark_model.108555_t, internal, 148, 295
-recovered GeneMark_model.108555_t, internal, 534, 668
-recovered GeneMark_model.108555_t, internal, 766, 815
-recovered GeneMark_model.108555_t, internal, 923, 1305
-recovered GeneMark_model.108555_t, internal, 1334, 1381
-recovered GeneMark_model.108555_t, internal, 2201, 2266
-recovered GeneMark_model.108555_t, internal, 2506, 2769
-recovered GeneMark_model.108555_t, internal, 2790, 2825
-recovered GeneMark_model.108555_t, internal, 2850, 2897
-recovered GeneMark_model.108555_t, internal, 3013, 3114

-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 33, 160
Couldn't classify 2978, 3108
Sorry, prediction snap_scaffold_890-snap.2-T1 fails validation.
(GTC)	 AG	33-160	GT	CTG
(ACT)	 AG	1734-1816	GT	AGG
(TCT)	 AG	2978-3108	GT	AGG
-recovered snap_scaffold_890-snap.2-T1, internal, 33, 160
-recovered snap_scaffold_890-snap.2-T1, internal, 1734, 1816
-recovered snap_scaffold_890-snap.2-T1, internal, 2978, 3108
Valid prediction for GeneMark_model.108556_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 2355, rend_intergenic: 943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 4018, rend_intergenic: 2528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 4050
-exon list size: 39


building trellis

2.4    
4.9    
7.3    
9.8    
12.2    
14.6    
17.1    
19.5    
22.0    
24.4    
26.8    
29.3    
31.7    
34.1    
36.6    
39.0    
41.5    
43.9    
46.3    
48.8    
51.2    
53.7    
56.1    
58.5    
61.0    
63.4    
65.9    
68.3    
70.7    
73.2    
75.6    
78.0    
80.5    
82.9    
85.4    
87.8    
90.2    
92.7    
95.1    
97.6    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 2355, rend_intergenic: 943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 4018, rend_intergenic: 2528  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