-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_335

-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 7064, 7186
Sorry, prediction GlimmerHMM_glimmerT_61722-T1 fails validation.
(ATG)	 AC	6171-6341	GT	CGG
(GTG)	 AG	6812-6934	GT	AGG
(GTG)	 AG	7064-7186	GT	AGG
-recovered GlimmerHMM_glimmerT_61722-T1, initial, 6171, 6341
-recovered GlimmerHMM_glimmerT_61722-T1, internal, 6812, 6934
-recovered GlimmerHMM_glimmerT_61722-T1, internal, 7064, 7186
Valid prediction for GlimmerHMM_glimmerT_61720-T1
Valid prediction for GeneMark_model.107339_t
Couldn't classify 211, 357
Sorry, prediction GeneMark_model.107338_t fails validation.
(CTG)	 AG	211-357	GT	AGG
(ATC)	 AG	624-732	GT	AGG
(GTG)	 AG	1865-2010	TG	GAT
-recovered GeneMark_model.107338_t, terminal, 1865, 2010
-recovered GeneMark_model.107338_t, internal, 211, 357
-recovered GeneMark_model.107338_t, internal, 624, 732
Couldn't classify 211, 357
Couldn't classify 7064, 7186
Sorry, prediction Augustus_model.g41026.t1 fails validation.
(CTG)	 AG	211-357	GT	AGG
(ATC)	 AG	624-732	GT	AGG
(GTG)	 AG	1865-1968	GT	AGG
(ATC)	 AG	5582-5668	GT	AGG
(TGT)	 AG	5896-6048	GT	TGG
(GTG)	 AG	6159-6341	GT	CGG
(GTG)	 AG	6812-6934	GT	AGG
(GTG)	 AG	7064-7186	GT	AGG
-recovered Augustus_model.g41026.t1, internal, 211, 357
-recovered Augustus_model.g41026.t1, internal, 624, 732
-recovered Augustus_model.g41026.t1, internal, 1865, 1968
-recovered Augustus_model.g41026.t1, internal, 5582, 5668
-recovered Augustus_model.g41026.t1, internal, 5896, 6048
-recovered Augustus_model.g41026.t1, internal, 6159, 6341
-recovered Augustus_model.g41026.t1, internal, 6812, 6934
-recovered Augustus_model.g41026.t1, internal, 7064, 7186
Couldn't classify 211, 357
Couldn't classify 7064, 7186
Sorry, prediction snap_scaffold_335-snap.2-T1 fails validation.
(CTG)	 AG	211-357	GT	AGG
(ATC)	 AG	624-732	GT	AGG
(GTG)	 AG	1865-1968	GT	AGG
(ATC)	 AG	5582-5668	GT	AGG
(TGT)	 AG	5896-6048	GT	TGG
(GTG)	 AG	6159-6341	GT	CGG
(GTG)	 AG	6812-6934	GT	AGG
(GTG)	 AG	7064-7186	GT	AGG
-recovered snap_scaffold_335-snap.2-T1, internal, 211, 357
-recovered snap_scaffold_335-snap.2-T1, internal, 624, 732
-recovered snap_scaffold_335-snap.2-T1, internal, 1865, 1968
-recovered snap_scaffold_335-snap.2-T1, internal, 5582, 5668
-recovered snap_scaffold_335-snap.2-T1, internal, 5896, 6048
-recovered snap_scaffold_335-snap.2-T1, internal, 6159, 6341
-recovered snap_scaffold_335-snap.2-T1, internal, 6812, 6934
-recovered snap_scaffold_335-snap.2-T1, internal, 7064, 7186
Valid prediction for GlimmerHMM_glimmerT_61721-T1

-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 snap_scaffold_335-snap.3-T1
Couldn't classify 20, 121
Sorry, prediction GeneMark_model.107340_t fails validation.
(AGT)	 AG	20-121	GT	CAG
(AGA)	 AG	172-417	GT	CAG
(TCT)	 AG	447-563	GT	CAG
(AGA)	 AG	584-741	GT	CAG
(CCT)	 AG	773-777	CT	GAC
-recovered GeneMark_model.107340_t, terminal, 773, 777
-recovered GeneMark_model.107340_t, internal, 20, 121
-recovered GeneMark_model.107340_t, internal, 172, 417
-recovered GeneMark_model.107340_t, internal, 447, 563
-recovered GeneMark_model.107340_t, internal, 584, 741
Valid prediction for snap_scaffold_335-snap.1-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7388, rend_intergenic: 211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8020
-exon list size: 38


building trellis

2.5    
5.0    
7.5    
10.0    
12.5    
15.0    
17.5    
20.0    
22.5    
25.0    
27.5    
30.0    
32.5    
35.0    
37.5    
40.0    
42.5    
45.0    
47.5    
50.0    
52.5    
55.0    
57.5    
60.0    
62.5    
65.0    
67.5    
70.0    
72.5    
75.0    
77.5    
80.0    
82.5    
85.0    
87.5    
90.0    
92.5    
95.0    
97.5    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 7388, rend_intergenic: 211  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