-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_12922816-13148480

-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 Augustus_model.g25474.t1
Valid prediction for GeneMark_model.65323_t
Valid prediction for GeneMark_model.65336_t
Valid prediction for Augustus_model.g25470.t1
Valid prediction for snap_scaffold_15-snap.2631-T1
Valid prediction for snap_scaffold_15-snap.2624-T1
Valid prediction for Augustus_model.g25472.t1
Valid prediction for snap_scaffold_15-snap.2617-T1
Valid prediction for HiQ_model.g25476.t1
Valid prediction for Augustus_model.g25487.t1
Valid prediction for snap_scaffold_15-snap.2626-T1
Valid prediction for GeneMark_model.65344_t
Valid prediction for pasa_asmbl_14559.p1
Valid prediction for GeneMark_model.65333_t
Valid prediction for GlimmerHMM_glimmerT_38008-T1
Valid prediction for GlimmerHMM_glimmerT_38004-T1
Valid prediction for snap_scaffold_15-snap.2627-T1
Valid prediction for CodingQuarry_transcript_18148-T1
Valid prediction for snap_scaffold_15-snap.2642-T1
Valid prediction for GlimmerHMM_glimmerT_38006-T1
Valid prediction for GeneMark_model.65342_t
Valid prediction for snap_scaffold_15-snap.2622-T1
Valid prediction for GeneMark_model.65341_t
Valid prediction for Augustus_model.g25479.t1
Valid prediction for GlimmerHMM_glimmerT_38020-T1
Valid prediction for pasa_asmbl_14556.p1
Valid prediction for GeneMark_model.65320_t
Valid prediction for GlimmerHMM_glimmerT_37995-T1
Valid prediction for GlimmerHMM_glimmerT_38019-T1
Valid prediction for snap_scaffold_15-snap.2616-T1
Valid prediction for GeneMark_model.65335_t
Valid prediction for GlimmerHMM_glimmerT_37997-T1
Valid prediction for snap_scaffold_15-snap.2628-T1
Valid prediction for Augustus_model.g25485.t1
Valid prediction for GlimmerHMM_glimmerT_38007-T1
Valid prediction for snap_scaffold_15-snap.2640-T1
Valid prediction for snap_scaffold_15-snap.2618-T1
Valid prediction for GlimmerHMM_glimmerT_38002-T1
Valid prediction for GlimmerHMM_glimmerT_37996-T1
Valid prediction for GlimmerHMM_glimmerT_38003-T1
Valid prediction for GeneMark_model.65325_t
Valid prediction for GlimmerHMM_glimmerT_38010-T1
Valid prediction for GlimmerHMM_glimmerT_38015-T1
Valid prediction for GeneMark_model.65332_t
Valid prediction for GeneMark_model.65327_t
Valid prediction for GeneMark_model.65324_t
Valid prediction for snap_scaffold_15-snap.2620-T1
Valid prediction for GlimmerHMM_glimmerT_38013-T1
Valid prediction for GeneMark_model.65331_t
Valid prediction for GeneMark_model.65346_t
Valid prediction for GeneMark_model.65322_t
Valid prediction for Augustus_model.g25477.t1
Valid prediction for GlimmerHMM_glimmerT_37994-T1
Valid prediction for GlimmerHMM_glimmerT_38000-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 GeneMark_model.65334_t
Valid prediction for GlimmerHMM_glimmerT_38017-T1
Couldn't classify 72159, 72261
Couldn't classify 75711, 75785
Sorry, prediction pasa_asmbl_15631.p1 fails validation.
(GCT)	 CA	72159-72261	GT	TGG
(AAC)	 AG	72369-72458	GT	AGG
(ATC)	 AG	72574-72739	GT	AGG
(GCC)	 AG	73000-73175	GT	TAG
(GTG)	 AG	73277-73431	GT	GGG
(ATT)	 AG	73531-73593	GT	GGG
(GAC)	 AG	73886-74005	GT	AGG
(GTG)	 AG	74327-74503	GT	AGG
(GTG)	 AG	75147-75230	GT	AGG
(ATG)	 AG	75337-75420	GT	AGG
(GTT)	 AG	75711-75785	GT	TGG
-recovered pasa_asmbl_15631.p1, initial, 75337, 75420
-recovered pasa_asmbl_15631.p1, internal, 72369, 72458
-recovered pasa_asmbl_15631.p1, internal, 72574, 72739
-recovered pasa_asmbl_15631.p1, internal, 73000, 73175
-recovered pasa_asmbl_15631.p1, internal, 73277, 73431
-recovered pasa_asmbl_15631.p1, internal, 73531, 73593
-recovered pasa_asmbl_15631.p1, internal, 73886, 74005
-recovered pasa_asmbl_15631.p1, internal, 74327, 74503
-recovered pasa_asmbl_15631.p1, internal, 75147, 75230
-recovered pasa_asmbl_15631.p1, internal, 75337, 75420
-recovered pasa_asmbl_15631.p1, internal, 75711, 75785
Valid prediction for GlimmerHMM_glimmerT_37998-T1
Valid prediction for GeneMark_model.65319_t
Valid prediction for snap_scaffold_15-snap.2611-T1
Valid prediction for HiQ_model.g25478.t1
Valid prediction for Augustus_model.g25469.t1
Valid prediction for GlimmerHMM_glimmerT_38018-T1
Valid prediction for GeneMark_model.65329_t
Valid prediction for snap_scaffold_15-snap.2634-T1
Couldn't classify 69689, 70015
Sorry, prediction pasa_asmbl_15900.p1 fails validation.
(ACA)	 AT	69689-70015	GG	AGG
Valid prediction for GlimmerHMM_glimmerT_38009-T1
Valid prediction for pasa_asmbl_15627.p1
Valid prediction for snap_scaffold_15-snap.2637-T1
Valid prediction for snap_scaffold_15-snap.2630-T1
Couldn't classify 46421, 46691
Sorry, prediction pasa_asmbl_15635.p1 fails validation.
(GGC)	 CA	46421-46691	GT	CGG
(ACT)	 AG	49675-49919	CG	GAC
-recovered pasa_asmbl_15635.p1, terminal, 49675, 49919
Couldn't classify 66659, 66913
Couldn't classify 67338, 67475
Sorry, prediction pasa_asmbl_15887.p1 fails validation.
(AAT)	 CC	66659-66913	GT	AGG
(GAG)	 AG	67338-67475	CC	CAC
Valid prediction for snap_scaffold_15-snap.2615-T1
Valid prediction for snap_scaffold_15-snap.2613-T1
Valid prediction for snap_scaffold_15-snap.2633-T1
Valid prediction for HiQ_model.g25483.t1
Valid prediction for GeneMark_model.65326_t
Valid prediction for GlimmerHMM_glimmerT_38016-T1
Valid prediction for GeneMark_model.65345_t
Valid prediction for Augustus_model.g25475.t1
Valid prediction for snap_scaffold_15-snap.2636-T1
Valid prediction for Augustus_model.g25471.t1
Valid prediction for Augustus_model.g25484.t1
Valid prediction for snap_scaffold_15-snap.2632-T1
Valid prediction for GeneMark_model.65330_t
Valid prediction for Augustus_model.g25468.t1
Valid prediction for GeneMark_model.65328_t
Valid prediction for GlimmerHMM_glimmerT_38012-T1
Valid prediction for GeneMark_model.65340_t
Valid prediction for HiQ_model.g25480.t1
Valid prediction for GlimmerHMM_glimmerT_37992-T1
Valid prediction for GeneMark_model.65321_t
Valid prediction for pasa_asmbl_15628.p1
Valid prediction for GlimmerHMM_glimmerT_38011-T1
Valid prediction for Augustus_model.g25473.t1
Valid prediction for CodingQuarry_transcript_18150-T1
Valid prediction for GeneMark_model.65316_t
Valid prediction for GlimmerHMM_glimmerT_37999-T1
Valid prediction for GlimmerHMM_glimmerT_38005-T1
Valid prediction for snap_scaffold_15-snap.2621-T1
Valid prediction for snap_scaffold_15-snap.2612-T1
Valid prediction for snap_scaffold_15-snap.2629-T1
Valid prediction for GlimmerHMM_glimmerT_38001-T1
Valid prediction for snap_scaffold_15-snap.2614-T1
Valid prediction for GeneMark_model.65343_t
Valid prediction for GeneMark_model.65318_t
Valid prediction for snap_scaffold_15-snap.2638-T1
Valid prediction for snap_scaffold_15-snap.2610-T1
Valid prediction for GlimmerHMM_glimmerT_37993-T1
Valid prediction for Augustus_model.g25481.t1
Valid prediction for snap_scaffold_15-snap.2635-T1
Valid prediction for CodingQuarry_transcript_18149-T1
Valid prediction for Augustus_model.g25482.t1
Valid prediction for GeneMark_model.65337_t
Valid prediction for snap_scaffold_15-snap.2623-T1
Valid prediction for GeneMark_model.65338_t
Valid prediction for GeneMark_model.65339_t
Valid prediction for snap_scaffold_15-snap.2625-T1
Valid prediction for snap_scaffold_15-snap.2641-T1
Valid prediction for snap_scaffold_15-snap.2619-T1
Valid prediction for Augustus_model.g25486.t1
Valid prediction for CodingQuarry_transcript_18151-T1
Valid prediction for snap_scaffold_15-snap.2639-T1
Couldn't classify 70850, 71296
Sorry, prediction pasa_asmbl_15632.p2 fails validation.
(CAC)	 CC	70850-71296	TA	CTT
Valid prediction for GlimmerHMM_glimmerT_37991-T1
Valid prediction for GeneMark_model.65317_t
Valid prediction for GlimmerHMM_glimmerT_38014-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42614, rend_intergenic: 39740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53653, rend_intergenic: 53297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225665
-exon list size: 400


building trellis

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91.3    
91.5    
91.8    
92.0    
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93.0    
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94.0    
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95.3    
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96.0    
96.3    
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97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 42614, rend_intergenic: 39740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53653, rend_intergenic: 53297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13139
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 12970