-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_1495374-1660571

-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 snap_scaffold_13-snap.277-T1
Valid prediction for GlimmerHMM_glimmerT_31104-T1
Valid prediction for snap_scaffold_13-snap.288-T1
Valid prediction for snap_scaffold_13-snap.284-T1
Valid prediction for GlimmerHMM_glimmerT_31103-T1
Valid prediction for Augustus_model.g20659.t1
Valid prediction for GlimmerHMM_glimmerT_31101-T1
Valid prediction for snap_scaffold_13-snap.276-T1
Valid prediction for CodingQuarry_transcript_12871-T1
Valid prediction for snap_scaffold_13-snap.275-T1
Valid prediction for HiQ_model.g20658.t1
Valid prediction for snap_scaffold_13-snap.286-T1
Valid prediction for GlimmerHMM_glimmerT_31098-T1
Valid prediction for snap_scaffold_13-snap.274-T1
Valid prediction for snap_scaffold_13-snap.281-T1
Valid prediction for Augustus_model.g20655.t1
Valid prediction for GlimmerHMM_glimmerT_31100-T1
Valid prediction for snap_scaffold_13-snap.297-T1
Valid prediction for snap_scaffold_13-snap.282-T1
Valid prediction for pasa_asmbl_10565.p1
Valid prediction for snap_scaffold_13-snap.290-T1
Valid prediction for snap_scaffold_13-snap.285-T1
Valid prediction for GlimmerHMM_glimmerT_31105-T1
Valid prediction for Augustus_model.g20660.t1
Valid prediction for snap_scaffold_13-snap.278-T1
Valid prediction for GlimmerHMM_glimmerT_31111-T1
Valid prediction for GlimmerHMM_glimmerT_31112-T1
Valid prediction for snap_scaffold_13-snap.270-T1
Valid prediction for snap_scaffold_13-snap.293-T1
Valid prediction for snap_scaffold_13-snap.273-T1
Valid prediction for snap_scaffold_13-snap.279-T1
Valid prediction for Augustus_model.g20665.t1
Valid prediction for snap_scaffold_13-snap.272-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_13-snap.280-T1
Valid prediction for Augustus_model.g20666.t1
Valid prediction for GlimmerHMM_glimmerT_31114-T1
Valid prediction for snap_scaffold_13-snap.299-T1
Valid prediction for snap_scaffold_13-snap.291-T1
Valid prediction for snap_scaffold_13-snap.283-T1
Valid prediction for snap_scaffold_13-snap.292-T1
Valid prediction for snap_scaffold_13-snap.295-T1
Valid prediction for Augustus_model.g20656.t1
Valid prediction for snap_scaffold_13-snap.300-T1
Valid prediction for pasa_asmbl_9414.p1
Valid prediction for Augustus_model.g20667.t1
Valid prediction for CodingQuarry_transcript_12870-T1
Valid prediction for Augustus_model.g20668.t1
Valid prediction for GlimmerHMM_glimmerT_31102-T1
Valid prediction for GlimmerHMM_glimmerT_31096-T1
Valid prediction for snap_scaffold_13-snap.289-T1
Valid prediction for GlimmerHMM_glimmerT_31107-T1
Valid prediction for GlimmerHMM_glimmerT_31097-T1
Valid prediction for Augustus_model.g20664.t1
Valid prediction for GlimmerHMM_glimmerT_31109-T1
Valid prediction for snap_scaffold_13-snap.287-T1
Valid prediction for CodingQuarry_transcript_12869-T1
Valid prediction for CodingQuarry_transcript_12868-T1
Valid prediction for GlimmerHMM_glimmerT_31099-T1
Valid prediction for GlimmerHMM_glimmerT_31110-T1
Valid prediction for snap_scaffold_13-snap.302-T1
Valid prediction for Augustus_model.g20661.t1
Valid prediction for Augustus_model.g20663.t1
Couldn't classify 22443, 22610
Sorry, prediction pasa_asmbl_9420.p1 fails validation.
(CAG)	 TC	22443-22610	GT	AGG
(GGA)	 AG	25472-25678	GC	AGG
-recovered pasa_asmbl_9420.p1, terminal, 25472, 25678
-recovered pasa_asmbl_9420.p1, internal, 25472, 25678
Valid prediction for GlimmerHMM_glimmerT_31113-T1
Valid prediction for HiQ_model.g20662.t1
Valid prediction for snap_scaffold_13-snap.296-T1
Valid prediction for HiQ_model.g20657.t1
Valid prediction for snap_scaffold_13-snap.301-T1
Valid prediction for snap_scaffold_13-snap.271-T1
Valid prediction for Augustus_model.g20654.t1
Valid prediction for snap_scaffold_13-snap.294-T1
Valid prediction for GlimmerHMM_glimmerT_31108-T1
Valid prediction for snap_scaffold_13-snap.298-T1
Couldn't classify 18443, 18582
Sorry, prediction pasa_asmbl_9421.p1 fails validation.
(ATG)	 AC	12014-12083	GT	AGG
(GGA)	 AG	12382-12554	GT	AGG
(AAA)	 AG	13762-13899	GT	CGG
(TTC)	 AG	14376-14561	GT	AGG
(CCA)	 AG	14925-15178	GT	AGG
(GTA)	 AG	15307-15449	GT	CGG
(GCA)	 AG	16635-16868	GT	CGG
(GTG)	 AG	17994-18227	GT	CAG
(TCC)	 AG	18443-18582	GT	AGG
-recovered pasa_asmbl_9421.p1, initial, 12014, 12083
-recovered pasa_asmbl_9421.p1, internal, 12382, 12554
-recovered pasa_asmbl_9421.p1, internal, 13762, 13899
-recovered pasa_asmbl_9421.p1, internal, 14376, 14561
-recovered pasa_asmbl_9421.p1, internal, 14925, 15178
-recovered pasa_asmbl_9421.p1, internal, 15307, 15449
-recovered pasa_asmbl_9421.p1, internal, 16635, 16868
-recovered pasa_asmbl_9421.p1, internal, 17994, 18227
-recovered pasa_asmbl_9421.p1, internal, 18443, 18582
Valid prediction for GlimmerHMM_glimmerT_31106-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10050, rend_intergenic: 7024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45198, rend_intergenic: 42995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61444, rend_intergenic: 59268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147099, rend_intergenic: 141170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165198
-exon list size: 217


building trellis

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72.6    
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74.9    
75.3    
75.8    
76.3    
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79.0    
79.5    
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81.3    
81.7    
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83.1    
83.6    
84.0    
84.5    
84.9    
85.4    
85.8    
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88.1    
88.6    
89.0    
89.5    
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90.9    
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91.8    
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93.6    
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95.4    
95.9    
96.3    
96.8    
97.3    
97.7    
98.2    
98.6    
99.1    
99.5    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 10050, rend_intergenic: 7024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45198, rend_intergenic: 42995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61444, rend_intergenic: 59268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147099, rend_intergenic: 141170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support