-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_322

-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 548, 607
Sorry, prediction Augustus_model.g41011.t1 fails validation.
(TCT)	 AG	548-607	GT	ATG
(ATT)	 AG	749-875	GT	AGG
(TTG)	 AG	1482-1590	GC	AGG
-recovered Augustus_model.g41011.t1, terminal, 1482, 1590
-recovered Augustus_model.g41011.t1, internal, 548, 607
-recovered Augustus_model.g41011.t1, internal, 749, 875
-recovered Augustus_model.g41011.t1, internal, 1482, 1590
Valid prediction for Augustus_model.g41013.t1
Valid prediction for GlimmerHMM_glimmerT_61697-T1
Couldn't classify 557, 628
Sorry, prediction GeneMark_model.107303_t fails validation.
(TGG)	 AG	557-628	GT	AGG
(ATT)	 AG	749-927	GT	AGG
(GTA)	 AG	1052-1141	AA	AGA
-recovered GeneMark_model.107303_t, terminal, 1052, 1141
-recovered GeneMark_model.107303_t, internal, 557, 628
-recovered GeneMark_model.107303_t, internal, 749, 927
Valid prediction for GeneMark_model.107307_t
Valid prediction for pasa_asmbl_40923.p1
Couldn't classify 548, 628
Sorry, prediction snap_scaffold_322-snap.1-T1 fails validation.
(TCT)	 AG	548-628	GT	AGG
(ATT)	 AG	749-940	GT	CGG
(TTG)	 AG	1482-1584	GT	GGG
(GAC)	 AG	3811-3821	GT	CGG
(GGT)	 AG	4453-4565	GT	TGG
(GCT)	 AG	5539-5612	GT	TTG
(CGC)	 AG	6473-6620	AG	AAA
-recovered snap_scaffold_322-snap.1-T1, terminal, 6473, 6620
-recovered snap_scaffold_322-snap.1-T1, internal, 548, 628
-recovered snap_scaffold_322-snap.1-T1, internal, 749, 940
-recovered snap_scaffold_322-snap.1-T1, internal, 1482, 1584
-recovered snap_scaffold_322-snap.1-T1, internal, 3811, 3821
-recovered snap_scaffold_322-snap.1-T1, internal, 4453, 4565
-recovered snap_scaffold_322-snap.1-T1, internal, 5539, 5612
Valid prediction for GlimmerHMM_glimmerT_61695-T1
Valid prediction for snap_scaffold_322-snap.3-T1
Valid prediction for GeneMark_model.107305_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: -)Valid prediction for HiQ_model.g41012.t1
Valid prediction for GlimmerHMM_glimmerT_61694-T1
Couldn't classify 2191, 2259
Couldn't classify 2609, 2880
Sorry, prediction pasa_asmbl_40912.p1 fails validation.
(GTG)	 AA	2191-2259	GT	AGG
(TGC)	 AG	2335-2452	GT	AGG
(CCT)	 AG	2609-2880	GG	GGG
-recovered pasa_asmbl_40912.p1, internal, 2335, 2452
Valid prediction for GeneMark_model.107304_t
Valid prediction for GeneMark_model.107306_t
Valid prediction for GlimmerHMM_glimmerT_61696-T1
Valid prediction for snap_scaffold_322-snap.2-T1
Couldn't classify 7457, 7867
Sorry, prediction pasa_asmbl_40919.p2 fails validation.
(ATG)	 CC	7457-7867	CA	CAC

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6620, rend_intergenic: 4449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8147
-exon list size: 60


building trellis

1.6    
3.2    
4.8    
6.5    
8.1    
9.7    
11.3    
12.9    
14.5    
16.1    
17.7    
19.4    
21.0    
22.6    
24.2    
25.8    
27.4    
29.0    
30.6    
32.3    
33.9    
35.5    
37.1    
38.7    
40.3    
41.9    
43.5    
45.2    
46.8    
48.4    
50.0    
51.6    
53.2    
54.8    
56.5    
58.1    
59.7    
61.3    
62.9    
64.5    
66.1    
67.7    
69.4    
71.0    
72.6    
74.2    
75.8    
77.4    
79.0    
80.6    
82.3    
83.9    
85.5    
87.1    
88.7    
90.3    
91.9    
93.5    
95.2    
96.8    
98.4    
-found 4 predictions from path traversal
Error with prediction: snap lend_intergenic: 6620, rend_intergenic: 4449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support