-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_1266502-1465513

-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_5-snap.294-T1
Couldn't classify 79145, 79275
Couldn't classify 80500, 80642
Sorry, prediction pasa_asmbl_46468.p1 fails validation.
(CAG)	 TG	79145-79275	GT	AGG
(GTT)	 AG	79394-79526	GT	CTG
(ATC)	 AG	79994-80186	GT	GCG
(CGT)	 AG	80500-80642	GG	AAG
-recovered pasa_asmbl_46468.p1, internal, 79394, 79526
-recovered pasa_asmbl_46468.p1, internal, 79994, 80186
Valid prediction for GlimmerHMM_glimmerT_11462-T1
Valid prediction for GlimmerHMM_glimmerT_11468-T1
Valid prediction for GlimmerHMM_glimmerT_11460-T1
Valid prediction for snap_scaffold_5-snap.268-T1
Couldn't classify 75643, 75811
Couldn't classify 77055, 77135
Sorry, prediction pasa_asmbl_46354.p1 fails validation.
(GAC)	 GC	75643-75811	GT	ACG
(CGT)	 AG	76123-76235	GT	TGG
(CCT)	 AG	77055-77135	TG	AGT
-recovered pasa_asmbl_46354.p1, internal, 76123, 76235
Valid prediction for CodingQuarry_transcript_51986-T1
Valid prediction for snap_scaffold_5-snap.271-T1
Valid prediction for snap_scaffold_5-snap.281-T1
Valid prediction for GlimmerHMM_glimmerT_11464-T1
Valid prediction for snap_scaffold_5-snap.258-T1
Couldn't classify 108819, 108933
Sorry, prediction pasa_asmbl_45123.p1 fails validation.
(AAC)	 GG	108819-108933	GT	AGG
(GTG)	 AG	109657-109886	GT	TGG
(CCC)	 AG	109987-110179	GT	CGG
(ACC)	 AG	110463-110596	GT	AGG
(GCC)	 AG	111811-111969	GT	AGG
(GTG)	 AG	112208-112318	GT	AGG
(GTG)	 AG	112700-112810	GT	AGG
(TTC)	 AG	112970-113071	GT	AGG
(GTG)	 AG	113266-113406	GT	AGG
(AGG)	 AG	113791-113909	GT	CAG
(GGT)	 AG	114141-114284	GT	AGG
(GTT)	 AG	114674-114966	GT	AGG
(CTG)	 AG	115100-115210	GT	AGG
(GCG)	 AG	115449-115665	GT	TGG
(GTA)	 AG	115802-115954	GT	AGG
(GAA)	 AG	116229-116395	GT	GGG
(GGT)	 AG	116836-116996	GT	AGG
(GCC)	 AG	118545-118820	AG	GAA
-recovered pasa_asmbl_45123.p1, terminal, 118545, 118820
-recovered pasa_asmbl_45123.p1, internal, 109657, 109886
-recovered pasa_asmbl_45123.p1, internal, 109987, 110179
-recovered pasa_asmbl_45123.p1, internal, 110463, 110596
-recovered pasa_asmbl_45123.p1, internal, 111811, 111969
-recovered pasa_asmbl_45123.p1, internal, 112208, 112318
-recovered pasa_asmbl_45123.p1, internal, 112700, 112810
-recovered pasa_asmbl_45123.p1, internal, 112970, 113071
-recovered pasa_asmbl_45123.p1, internal, 113266, 113406
-recovered pasa_asmbl_45123.p1, internal, 113791, 113909
-recovered pasa_asmbl_45123.p1, internal, 114141, 114284
-recovered pasa_asmbl_45123.p1, internal, 114674, 114966
-recovered pasa_asmbl_45123.p1, internal, 115100, 115210
-recovered pasa_asmbl_45123.p1, internal, 115449, 115665
-recovered pasa_asmbl_45123.p1, internal, 115802, 115954
-recovered pasa_asmbl_45123.p1, internal, 116229, 116395
-recovered pasa_asmbl_45123.p1, internal, 116836, 116996
Valid prediction for Augustus_model.g7492.t1
Valid prediction for GlimmerHMM_glimmerT_11475-T1
Valid prediction for GlimmerHMM_glimmerT_11463-T1
Couldn't classify 73724, 73924
Couldn't classify 74550, 74669
Sorry, prediction pasa_asmbl_46477.p2 fails validation.
(CAG)	 AC	73724-73924	GT	TGG
(GTC)	 AG	74550-74669	AG	AGA
Valid prediction for snap_scaffold_5-snap.270-T1
Valid prediction for snap_scaffold_5-snap.278-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11466-T1
Valid prediction for GlimmerHMM_glimmerT_11471-T1
Couldn't classify 81774, 81814
Couldn't classify 87354, 87442
Sorry, prediction pasa_asmbl_45119.p1 fails validation.
(CGT)	 GC	81774-81814	GT	CAG
(CTG)	 AG	82039-82174	GT	AGG
(GGC)	 AG	84588-84740	GT	AGG
(CTC)	 AG	85225-85352	GT	AGG
(GTT)	 AG	85471-85603	GT	CCG
(ATC)	 AG	86073-86265	GT	GCG
(CGT)	 AG	86742-86885	GT	AGG
(CTT)	 AG	87354-87442	GT	TGG
-recovered pasa_asmbl_45119.p1, internal, 82039, 82174
-recovered pasa_asmbl_45119.p1, internal, 84588, 84740
-recovered pasa_asmbl_45119.p1, internal, 85225, 85352
-recovered pasa_asmbl_45119.p1, internal, 85471, 85603
-recovered pasa_asmbl_45119.p1, internal, 86073, 86265
-recovered pasa_asmbl_45119.p1, internal, 86742, 86885
-recovered pasa_asmbl_45119.p1, internal, 87354, 87442
Valid prediction for snap_scaffold_5-snap.259-T1
Valid prediction for snap_scaffold_5-snap.285-T1
Valid prediction for snap_scaffold_5-snap.256-T1
Valid prediction for GlimmerHMM_glimmerT_11472-T1
Valid prediction for GlimmerHMM_glimmerT_11455-T1
Valid prediction for Augustus_model.g7495.t1
Valid prediction for snap_scaffold_5-snap.288-T1
Valid prediction for Augustus_model.g7493.t1
Valid prediction for GlimmerHMM_glimmerT_11459-T1
Valid prediction for snap_scaffold_5-snap.260-T1
Valid prediction for Augustus_model.g7496.t1
Valid prediction for snap_scaffold_5-snap.295-T1
Valid prediction for Augustus_model.g7494.t1
Valid prediction for snap_scaffold_5-snap.276-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.283-T1
Valid prediction for Augustus_model.g7491.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_5-snap.267-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.286-T1
Valid prediction for snap_scaffold_5-snap.264-T1
Valid prediction for snap_scaffold_5-snap.297-T1
Valid prediction for snap_scaffold_5-snap.262-T1
Valid prediction for snap_scaffold_5-snap.266-T1
Valid prediction for snap_scaffold_5-snap.293-T1
Valid prediction for snap_scaffold_5-snap.292-T1
Valid prediction for snap_scaffold_5-snap.273-T1
Valid prediction for GlimmerHMM_glimmerT_11465-T1
Valid prediction for snap_scaffold_5-snap.289-T1
Valid prediction for snap_scaffold_5-snap.291-T1
Valid prediction for snap_scaffold_5-snap.279-T1
Valid prediction for snap_scaffold_5-snap.269-T1
Valid prediction for GlimmerHMM_glimmerT_11470-T1
Valid prediction for snap_scaffold_5-snap.277-T1
Valid prediction for snap_scaffold_5-snap.275-T1
Valid prediction for snap_scaffold_5-snap.263-T1
Valid prediction for GlimmerHMM_glimmerT_11467-T1
Valid prediction for snap_scaffold_5-snap.254-T1
Valid prediction for GlimmerHMM_glimmerT_11469-T1
Valid prediction for snap_scaffold_5-snap.261-T1
Valid prediction for GlimmerHMM_glimmerT_11474-T1
Valid prediction for snap_scaffold_5-snap.284-T1
Valid prediction for GlimmerHMM_glimmerT_11458-T1
Valid prediction for GlimmerHMM_glimmerT_11473-T1
Valid prediction for snap_scaffold_5-snap.282-T1
Valid prediction for snap_scaffold_5-snap.257-T1
Valid prediction for snap_scaffold_5-snap.280-T1
Couldn't classify 98504, 98941
Sorry, prediction pasa_asmbl_45120.p1 fails validation.
(CTG)	 TT	98504-98941	AC	AGA
Valid prediction for snap_scaffold_5-snap.272-T1
Valid prediction for snap_scaffold_5-snap.274-T1
Valid prediction for snap_scaffold_5-snap.296-T1
Valid prediction for GlimmerHMM_glimmerT_11461-T1
Valid prediction for snap_scaffold_5-snap.290-T1
Valid prediction for GlimmerHMM_glimmerT_11457-T1
Valid prediction for snap_scaffold_5-snap.287-T1
Valid prediction for snap_scaffold_5-snap.265-T1
Valid prediction for Augustus_model.g7490.t1
Valid prediction for snap_scaffold_5-snap.255-T1
Valid prediction for GlimmerHMM_glimmerT_11456-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5892, rend_intergenic: 4259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7982, rend_intergenic: 6882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15073, rend_intergenic: 8876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47513, rend_intergenic: 20252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53081, rend_intergenic: 49470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56645, rend_intergenic: 53169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98626, rend_intergenic: 70138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107141, rend_intergenic: 103455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118820, rend_intergenic: 108321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120390, rend_intergenic: 120375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123470, rend_intergenic: 120908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130395, rend_intergenic: 124591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139328, rend_intergenic: 132927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165956, rend_intergenic: 140196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193621, rend_intergenic: 182993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199012
-exon list size: 401


building trellis

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97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 5892, rend_intergenic: 4259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7982, rend_intergenic: 6882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15073, rend_intergenic: 8876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47513, rend_intergenic: 20252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53081, rend_intergenic: 49470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56645, rend_intergenic: 53169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98626, rend_intergenic: 70138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107141, rend_intergenic: 103455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118820, rend_intergenic: 108321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120390, rend_intergenic: 120375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123470, rend_intergenic: 120908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130395, rend_intergenic: 124591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139328, rend_intergenic: 132927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165956, rend_intergenic: 140196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193621, rend_intergenic: 182993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support