-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_13146817-13367042

-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 CodingQuarry_transcript_46210-T1
Valid prediction for GeneMark_model.12725_t
Valid prediction for snap_scaffold_3-snap.2551-T1
Valid prediction for snap_scaffold_3-snap.2559-T1
Valid prediction for snap_scaffold_3-snap.2555-T1
Valid prediction for GeneMark_model.12745_t
Valid prediction for GeneMark_model.12721_t
Valid prediction for GlimmerHMM_glimmerT_7737-T1
Valid prediction for snap_scaffold_3-snap.2565-T1
Valid prediction for GlimmerHMM_glimmerT_7722-T1
Valid prediction for HiQ_model.g5076.t1
Valid prediction for GlimmerHMM_glimmerT_7732-T1
Valid prediction for GlimmerHMM_glimmerT_7733-T1
Valid prediction for snap_scaffold_3-snap.2578-T1
Valid prediction for Augustus_model.g5083.t1
Valid prediction for Augustus_model.g5090.t1
Valid prediction for snap_scaffold_3-snap.2572-T1
Valid prediction for Augustus_model.g5092.t1
Valid prediction for snap_scaffold_3-snap.2581-T1
Valid prediction for GlimmerHMM_glimmerT_7725-T1
Valid prediction for GeneMark_model.12737_t
Valid prediction for GlimmerHMM_glimmerT_7734-T1
Valid prediction for GlimmerHMM_glimmerT_7718-T1
Valid prediction for GlimmerHMM_glimmerT_7739-T1
Valid prediction for CodingQuarry_transcript_46208-T1
Valid prediction for Augustus_model.g5075.t1
Valid prediction for snap_scaffold_3-snap.2573-T1
Valid prediction for GeneMark_model.12743_t
Valid prediction for GlimmerHMM_glimmerT_7720-T1
Valid prediction for snap_scaffold_3-snap.2556-T1
Valid prediction for pasa_asmbl_40392.p1
Valid prediction for GeneMark_model.12728_t
Valid prediction for CodingQuarry_transcript_46212-T1
Valid prediction for snap_scaffold_3-snap.2566-T1
Couldn't classify 67309, 68157
Sorry, prediction pasa_asmbl_40396.p1 fails validation.
(GAG)	 CC	67309-68157	CT	ATC
Valid prediction for GlimmerHMM_glimmerT_7741-T1
Valid prediction for GlimmerHMM_glimmerT_7740-T1
Valid prediction for Augustus_model.g5081.t1
Valid prediction for snap_scaffold_3-snap.2561-T1
Valid prediction for CodingQuarry_transcript_46211-T1
Valid prediction for GeneMark_model.12727_t
Valid prediction for Augustus_model.g5082.t1
Valid prediction for GeneMark_model.12720_t
Valid prediction for GeneMark_model.12735_t
Valid prediction for snap_scaffold_3-snap.2577-T1
Valid prediction for Augustus_model.g5073.t1
Valid prediction for CodingQuarry_transcript_46209-T1
Valid prediction for GeneMark_model.12746_t
Valid prediction for GlimmerHMM_glimmerT_7729-T1
Valid prediction for snap_scaffold_3-snap.2574-T1
Valid prediction for Augustus_model.g5086.t1
Valid prediction for snap_scaffold_3-snap.2550-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for pasa_asmbl_40386.p1
Valid prediction for Augustus_model.g5078.t1
Valid prediction for snap_scaffold_3-snap.2549-T1
Valid prediction for Augustus_model.g5087.t1
Valid prediction for GeneMark_model.12718_t
Valid prediction for GlimmerHMM_glimmerT_7727-T1
Valid prediction for GeneMark_model.12716_t
Valid prediction for snap_scaffold_3-snap.2571-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_3-snap.2582-T1
Valid prediction for snap_scaffold_3-snap.2560-T1
Valid prediction for GeneMark_model.12740_t
Valid prediction for snap_scaffold_3-snap.2563-T1
Valid prediction for GlimmerHMM_glimmerT_7726-T1
Couldn't classify 39400, 39453
Sorry, prediction pasa_asmbl_39200.p1 fails validation.
(TCA)	 GN	39400-39453	GT	AGG
(ACT)	 AG	39561-39656	GT	CTG
(GAG)	 AG	39738-39872	GT	AGG
(AAA)	 AG	40026-40046	AG	GAA
-recovered pasa_asmbl_39200.p1, terminal, 40026, 40046
-recovered pasa_asmbl_39200.p1, internal, 39561, 39656
-recovered pasa_asmbl_39200.p1, internal, 39738, 39872
Valid prediction for snap_scaffold_3-snap.2579-T1
Valid prediction for GlimmerHMM_glimmerT_7730-T1
Valid prediction for HiQ_model.g5091.t1
Valid prediction for pasa_asmbl_39203.p1
Valid prediction for Augustus_model.g5074.t1
Valid prediction for GeneMark_model.12736_t
Valid prediction for GlimmerHMM_glimmerT_7735-T1
Valid prediction for snap_scaffold_3-snap.2570-T1
Valid prediction for Augustus_model.g5085.t1
Valid prediction for Augustus_model.g5077.t1
Valid prediction for GeneMark_model.12733_t
Valid prediction for Augustus_model.g5088.t1
Valid prediction for GlimmerHMM_glimmerT_7731-T1
Valid prediction for GeneMark_model.12732_t
Valid prediction for snap_scaffold_3-snap.2575-T1
Valid prediction for GeneMark_model.12742_t
Valid prediction for Augustus_model.g5089.t1
Valid prediction for snap_scaffold_3-snap.2569-T1
Valid prediction for GlimmerHMM_glimmerT_7738-T1
Valid prediction for GeneMark_model.12717_t
Valid prediction for GlimmerHMM_glimmerT_7724-T1
Valid prediction for GlimmerHMM_glimmerT_7719-T1
Valid prediction for GeneMark_model.12726_t
Valid prediction for GlimmerHMM_glimmerT_7728-T1
Valid prediction for snap_scaffold_3-snap.2552-T1
Valid prediction for snap_scaffold_3-snap.2553-T1
Valid prediction for snap_scaffold_3-snap.2557-T1
Valid prediction for GlimmerHMM_glimmerT_7721-T1
Valid prediction for CodingQuarry_transcript_46215-T1
Valid prediction for snap_scaffold_3-snap.2583-T1
Valid prediction for Augustus_model.g5079.t1
Valid prediction for Augustus_model.g5080.t1
Valid prediction for GeneMark_model.12723_t
Valid prediction for GeneMark_model.12729_t
Valid prediction for Augustus_model.g5084.t1
Valid prediction for GeneMark_model.12722_t
Valid prediction for GlimmerHMM_glimmerT_7717-T1
Valid prediction for GeneMark_model.12719_t
Valid prediction for GeneMark_model.12734_t
Valid prediction for GeneMark_model.12744_t
Valid prediction for snap_scaffold_3-snap.2567-T1
Valid prediction for snap_scaffold_3-snap.2576-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7736-T1
Valid prediction for GeneMark_model.12731_t
Valid prediction for snap_scaffold_3-snap.2580-T1
Valid prediction for GeneMark_model.12741_t
Valid prediction for GlimmerHMM_glimmerT_7723-T1
Valid prediction for snap_scaffold_3-snap.2564-T1
Valid prediction for Augustus_model.g5072.t1
Valid prediction for GeneMark_model.12738_t
Valid prediction for CodingQuarry_transcript_46213-T1
Valid prediction for GeneMark_model.12730_t
Valid prediction for snap_scaffold_3-snap.2554-T1
Valid prediction for snap_scaffold_3-snap.2558-T1
Valid prediction for CodingQuarry_transcript_46214-T1
Valid prediction for snap_scaffold_3-snap.2568-T1
Valid prediction for snap_scaffold_3-snap.2562-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14900, rend_intergenic: 11225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220226
-exon list size: 364


building trellis

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48.1    
48.4    
48.6    
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53.6    
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88.0    
88.3    
88.5    
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89.1    
89.3    
89.6    
89.9    
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90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
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93.4    
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94.0    
94.3    
94.5    
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95.4    
95.6    
95.9    
96.2    
96.4    
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97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 14900, rend_intergenic: 11225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support