-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_305

-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.107245_t
Couldn't classify 1423, 1440
Couldn't classify 6137, 6493
Sorry, prediction snap_scaffold_305-snap.2-T1 fails validation.
(TCT)	 AG	1423-1440	GT	AGG
(GCG)	 AG	3436-3507	GT	AGG
(GGC)	 AG	5772-5946	GT	TCG
(GCT)	 AG	6137-6493	GT	AGG
-recovered snap_scaffold_305-snap.2-T1, internal, 1423, 1440
-recovered snap_scaffold_305-snap.2-T1, internal, 3436, 3507
-recovered snap_scaffold_305-snap.2-T1, internal, 5772, 5946
-recovered snap_scaffold_305-snap.2-T1, internal, 6137, 6493
Couldn't classify 563, 568
Sorry, prediction GeneMark_model.107243_t fails validation.
(ACA)	 AG	563-568	GT	GGG
(AGG)	 AG	598-624	GT	AGG
(AGA)	 AG	647-658	GT	AGG
(TAC)	 AG	685-702	GT	AGG
(AGA)	 AG	724-828	GT	AGG
(AGA)	 AG	851-883	GT	AAG
(GGG)	 AG	906-957	AG	AGA
-recovered GeneMark_model.107243_t, terminal, 647, 658
-recovered GeneMark_model.107243_t, terminal, 906, 957
-recovered GeneMark_model.107243_t, internal, 563, 568
-recovered GeneMark_model.107243_t, internal, 598, 624
-recovered GeneMark_model.107243_t, internal, 647, 658
-recovered GeneMark_model.107243_t, internal, 685, 702
-recovered GeneMark_model.107243_t, internal, 724, 828
-recovered GeneMark_model.107243_t, internal, 851, 883
Couldn't classify 8239, 8291
Sorry, prediction GeneMark_model.107247_t fails validation.
(ATG)	 AC	5165-5196	GT	AGG
(AGA)	 AG	5221-5256	GT	AGG
(GGC)	 AG	5290-5328	GT	AGG
(GCA)	 AG	5361-5408	GT	AGG
(ACA)	 AG	5431-5454	GT	AGG
(GCA)	 AG	5479-5490	GT	AGG
(AGA)	 AG	5515-5550	GT	AGG
(GGA)	 AG	6254-6274	GT	GGG
(AGG)	 AG	6296-6346	GT	GGG
(AGG)	 AG	6370-6390	GT	GGG
(AGG)	 AG	6422-6493	GT	AGG
(GGC)	 AG	6519-6527	GT	GAG
(AGT)	 AG	6553-6561	GT	GAG
(AGT)	 AG	6584-6643	GT	GAG
(AGA)	 AG	6677-6691	GT	GAG
(GTC)	 AG	6896-6904	GT	CAG
(GGG)	 AG	8172-8210	GT	GGG
(GGA)	 AG	8239-8291	GT	GGG
-recovered GeneMark_model.107247_t, initial, 5165, 5196
-recovered GeneMark_model.107247_t, terminal, 5479, 5490
-recovered GeneMark_model.107247_t, internal, 5221, 5256
-recovered GeneMark_model.107247_t, internal, 5290, 5328
-recovered GeneMark_model.107247_t, internal, 5361, 5408
-recovered GeneMark_model.107247_t, internal, 5431, 5454
-recovered GeneMark_model.107247_t, internal, 5479, 5490
-recovered GeneMark_model.107247_t, internal, 5515, 5550
-recovered GeneMark_model.107247_t, internal, 6254, 6274
-recovered GeneMark_model.107247_t, internal, 6296, 6346
-recovered GeneMark_model.107247_t, internal, 6370, 6390
-recovered GeneMark_model.107247_t, internal, 6422, 6493
-recovered GeneMark_model.107247_t, internal, 6519, 6527
-recovered GeneMark_model.107247_t, internal, 6553, 6561
-recovered GeneMark_model.107247_t, internal, 6584, 6643
-recovered GeneMark_model.107247_t, internal, 6677, 6691
-recovered GeneMark_model.107247_t, internal, 6896, 6904
-recovered GeneMark_model.107247_t, internal, 8172, 8210
-recovered GeneMark_model.107247_t, internal, 8239, 8291

-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 2291, 2686
Sorry, prediction snap_scaffold_305-snap.1-T1 fails validation.
(CCG)	 AG	2291-2686	GT	ATG
(ACC)	 AG	4882-4942	GT	CTG
(GTG)	 AG	6909-7079	AA	AGA
-recovered snap_scaffold_305-snap.1-T1, terminal, 6909, 7079
-recovered snap_scaffold_305-snap.1-T1, internal, 2291, 2686
-recovered snap_scaffold_305-snap.1-T1, internal, 4882, 4942
Valid prediction for GeneMark_model.107244_t
Valid prediction for GlimmerHMM_glimmerT_61667-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61667-T1 2282-2699-terminal-1 is invalid.
Valid prediction for GeneMark_model.107246_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6085, rend_intergenic: 1423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8375
-exon list size: 86


building trellis

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23.9    
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28.4    
29.5    
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31.8    
33.0    
34.1    
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48.9    
50.0    
51.1    
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53.4    
54.5    
55.7    
56.8    
58.0    
59.1    
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61.4    
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63.6    
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65.9    
67.0    
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71.6    
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73.9    
75.0    
76.1    
77.3    
78.4    
79.5    
80.7    
81.8    
83.0    
84.1    
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86.4    
87.5    
88.6    
89.8    
90.9    
92.0    
93.2    
94.3    
95.5    
96.6    
97.7    
98.9    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 6085, rend_intergenic: 1423  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