-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_258

-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 GeneMark_model.107104_t
Couldn't classify 6454, 6772
Sorry, prediction snap_scaffold_258-snap.3-T1 fails validation.
(ATG)	 GC	3745-3847	GT	CAG
(GAG)	 AG	4000-4468	GT	TTG
(TTT)	 AG	4691-4803	GT	CGG
(CAG)	 AG	6332-6415	GT	ACG
(GAT)	 AG	6454-6772	GT	TGG
-recovered snap_scaffold_258-snap.3-T1, initial, 3745, 3847
-recovered snap_scaffold_258-snap.3-T1, internal, 4000, 4468
-recovered snap_scaffold_258-snap.3-T1, internal, 4691, 4803
-recovered snap_scaffold_258-snap.3-T1, internal, 6332, 6415
-recovered snap_scaffold_258-snap.3-T1, internal, 6454, 6772
Couldn't classify 8600, 8680
Sorry, prediction GeneMark_model.107105_t fails validation.
(ATG)	 AC	5675-5688	GT	GAG
(GGA)	 AG	5785-5826	GT	GGG
(GGA)	 AG	5852-6127	GT	CAG
(GCA)	 AG	6149-6233	GT	CAG
(CGT)	 AG	6301-6415	GT	ACG
(GAT)	 AG	6454-6703	GT	GAG
(GCA)	 AG	6757-6793	GT	TGG
(TGT)	 AG	7508-7608	GT	AAG
(TGT)	 AG	7662-7841	GT	AAG
(TGT)	 AG	7895-8104	GT	AAG
(TCT)	 AG	8207-8305	GT	AAG
(TCT)	 AG	8456-8563	GT	CTG
(ACC)	 AG	8600-8680	GT	GCG
-recovered GeneMark_model.107105_t, initial, 5675, 5688
add_exon() Sorry, GeneMark_model.107105_t 6454-6703-terminal-3 is invalid.
-recovered GeneMark_model.107105_t, terminal, 6454, 6703
-recovered GeneMark_model.107105_t, internal, 5785, 5826
-recovered GeneMark_model.107105_t, internal, 5852, 6127
-recovered GeneMark_model.107105_t, internal, 6149, 6233
-recovered GeneMark_model.107105_t, internal, 6301, 6415
-recovered GeneMark_model.107105_t, internal, 6454, 6703
-recovered GeneMark_model.107105_t, internal, 6757, 6793
-recovered GeneMark_model.107105_t, internal, 7508, 7608
-recovered GeneMark_model.107105_t, internal, 7662, 7841
-recovered GeneMark_model.107105_t, internal, 7895, 8104
-recovered GeneMark_model.107105_t, internal, 8207, 8305
-recovered GeneMark_model.107105_t, internal, 8456, 8563
-recovered GeneMark_model.107105_t, internal, 8600, 8680

-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 8488, 8597
Sorry, prediction Augustus_model.g40956.t1 fails validation.
(ATG)	 AG	6462-6467	GT	AGG
(CTT)	 AG	6591-6649	GT	AGG
(AGG)	 AG	7079-7200	GT	ATG
(GCC)	 AG	8488-8597	GT	CGG
-recovered Augustus_model.g40956.t1, initial, 6462, 6467
-recovered Augustus_model.g40956.t1, internal, 6462, 6467
-recovered Augustus_model.g40956.t1, internal, 6591, 6649
-recovered Augustus_model.g40956.t1, internal, 7079, 7200
-recovered Augustus_model.g40956.t1, internal, 8488, 8597
Valid prediction for snap_scaffold_258-snap.2-T1
Couldn't classify 8488, 8597
Sorry, prediction snap_scaffold_258-snap.1-T1 fails validation.
(ATG)	 GC	7251-7435	GT	AAG
(TGG)	 AG	7650-7711	GT	GGG
(GCC)	 AG	8488-8597	GT	CGG
-recovered snap_scaffold_258-snap.1-T1, initial, 7251, 7435
-recovered snap_scaffold_258-snap.1-T1, internal, 7650, 7711
-recovered snap_scaffold_258-snap.1-T1, internal, 8488, 8597
Valid prediction for Augustus_model.g40957.t1
Couldn't classify 8488, 8597
Sorry, prediction GeneMark_model.107102_t fails validation.
(ATG)	 GA	8310-8382	GT	AAG
(GCC)	 AG	8488-8597	GT	CGG
-recovered GeneMark_model.107102_t, initial, 8310, 8382
-recovered GeneMark_model.107102_t, internal, 8488, 8597
Valid prediction for GeneMark_model.107103_t
Valid prediction for GlimmerHMM_glimmerT_61594-T1
Couldn't classify 2499, 2740
Sorry, prediction snap_scaffold_258-snap.4-T1 fails validation.
(AGG)	 AG	2499-2740	GT	GGG
(ACC)	 AG	3874-3937	GT	ATG
(ATG)	 AG	4020-4166	TG	GAT
-recovered snap_scaffold_258-snap.4-T1, terminal, 4020, 4166
-recovered snap_scaffold_258-snap.4-T1, internal, 2499, 2740
-recovered snap_scaffold_258-snap.4-T1, internal, 3874, 3937

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6772, rend_intergenic: 4813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8978
-exon list size: 89


building trellis

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28.6    
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30.8    
31.9    
33.0    
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40.7    
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42.9    
44.0    
45.1    
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47.3    
48.4    
49.5    
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51.6    
52.7    
53.8    
54.9    
56.0    
57.1    
58.2    
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62.6    
63.7    
64.8    
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67.0    
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71.4    
72.5    
73.6    
74.7    
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76.9    
78.0    
79.1    
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81.3    
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84.6    
85.7    
86.8    
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89.0    
90.1    
91.2    
92.3    
93.4    
94.5    
95.6    
96.7    
97.8    
98.9    
-found 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 6772, rend_intergenic: 4813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support