-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_13574258-13781351

-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: +)Couldn't classify 52845, 53068
Sorry, prediction pasa_asmbl_12494.p1 fails validation.
(GGA)	 CA	52845-53068	GT	AAG
(GGA)	 AG	53254-53354	GT	GGG
(AGT)	 AG	53617-53736	GT	TGG
(ACT)	 AG	55144-55310	GT	CGG
(GGA)	 AG	56018-56089	TA	GAT
-recovered pasa_asmbl_12494.p1, terminal, 56018, 56089
-recovered pasa_asmbl_12494.p1, internal, 53254, 53354
-recovered pasa_asmbl_12494.p1, internal, 53617, 53736
-recovered pasa_asmbl_12494.p1, internal, 55144, 55310
Valid prediction for GlimmerHMM_glimmerT_35029-T1
Valid prediction for snap_scaffold_14-snap.2807-T1
Valid prediction for HiQ_model.g23427.t1
Valid prediction for pasa_asmbl_12490.p1
Valid prediction for GlimmerHMM_glimmerT_35037-T1
Valid prediction for Augustus_model.g23421.t1
Couldn't classify 104278, 104339
Sorry, prediction pasa_asmbl_12498.p1 fails validation.
(ATC)	 CC	104278-104339	GT	AGG
(GCC)	 AG	105774-105936	GT	AGG
(TTT)	 AG	106108-106241	GT	AGG
(CTC)	 AG	106344-106508	GT	AGG
(GCT)	 AG	106866-107046	GT	AGG
(TAC)	 AG	107183-107331	GT	AGG
(AGC)	 AG	107428-107598	GT	ATG
(GGT)	 AG	107895-108088	GT	CGG
(ACG)	 AG	108544-108687	GT	TGG
(AGG)	 AG	108858-108985	GT	GGG
(GAC)	 AG	109193-109302	GT	AAG
(AGA)	 AG	110190-110299	GT	AGG
(GTA)	 AG	110471-110574	AG	AGA
-recovered pasa_asmbl_12498.p1, terminal, 110471, 110574
-recovered pasa_asmbl_12498.p1, internal, 105774, 105936
-recovered pasa_asmbl_12498.p1, internal, 106108, 106241
-recovered pasa_asmbl_12498.p1, internal, 106344, 106508
-recovered pasa_asmbl_12498.p1, internal, 106866, 107046
-recovered pasa_asmbl_12498.p1, internal, 107183, 107331
-recovered pasa_asmbl_12498.p1, internal, 107428, 107598
-recovered pasa_asmbl_12498.p1, internal, 107895, 108088
-recovered pasa_asmbl_12498.p1, internal, 108544, 108687
-recovered pasa_asmbl_12498.p1, internal, 108858, 108985
-recovered pasa_asmbl_12498.p1, internal, 109193, 109302
-recovered pasa_asmbl_12498.p1, internal, 110190, 110299
Valid prediction for CodingQuarry_transcript_15920-T1
Couldn't classify 97713, 97879
Couldn't classify 99323, 99416
Sorry, prediction pasa_asmbl_12497.p1 fails validation.
(GTG)	 CA	97713-97879	GT	CGG
(GAC)	 AG	98388-98513	GT	AGG
(AGA)	 AG	98872-99004	GT	GAG
(GAA)	 AG	99099-99226	GT	AGG
(AGT)	 AG	99323-99416	AT	TGA
-recovered pasa_asmbl_12497.p1, internal, 98388, 98513
-recovered pasa_asmbl_12497.p1, internal, 98872, 99004
-recovered pasa_asmbl_12497.p1, internal, 99099, 99226
Valid prediction for GlimmerHMM_glimmerT_35035-T1
Valid prediction for CodingQuarry_transcript_15918-T1
Valid prediction for CodingQuarry_transcript_15917-T1
Valid prediction for snap_scaffold_14-snap.2833-T1
Valid prediction for snap_scaffold_14-snap.2809-T1
Valid prediction for snap_scaffold_14-snap.2829-T1
Valid prediction for pasa_asmbl_12495.p1
Valid prediction for snap_scaffold_14-snap.2830-T1
Couldn't classify 30352, 30468
Sorry, prediction pasa_asmbl_12489.p1 fails validation.
(ATG)	 AA	29197-29301	GT	CAG
(AAA)	 AG	29666-29821	GT	AGG
(AAA)	 AG	30352-30468	GT	AAG
-recovered pasa_asmbl_12489.p1, initial, 29197, 29301
-recovered pasa_asmbl_12489.p1, internal, 29666, 29821
-recovered pasa_asmbl_12489.p1, internal, 30352, 30468
Valid prediction for snap_scaffold_14-snap.2813-T1
Valid prediction for snap_scaffold_14-snap.2817-T1
Valid prediction for snap_scaffold_14-snap.2822-T1
Valid prediction for snap_scaffold_14-snap.2818-T1
Valid prediction for GlimmerHMM_glimmerT_35039-T1
Valid prediction for Augustus_model.g23426.t1
Valid prediction for snap_scaffold_14-snap.2796-T1
Couldn't classify 44140, 44220
Couldn't classify 46338, 46436
Sorry, prediction pasa_asmbl_12493.p1 fails validation.
(CGC)	 GA	44140-44220	GT	TGG
(GAT)	 AG	45335-45430	GT	AAG
(AAC)	 AG	45950-46039	GT	CTG
(AAG)	 AG	46338-46436	CT	GCC
-recovered pasa_asmbl_12493.p1, internal, 45335, 45430
-recovered pasa_asmbl_12493.p1, internal, 45950, 46039
Valid prediction for Augustus_model.g23436.t1
Valid prediction for GlimmerHMM_glimmerT_35016-T1
Valid prediction for Augustus_model.g23430.t1
Valid prediction for GlimmerHMM_glimmerT_35020-T1
Valid prediction for GlimmerHMM_glimmerT_35036-T1
Valid prediction for Augustus_model.g23434.t1
Valid prediction for HiQ_model.g23419.t1
Valid prediction for snap_scaffold_14-snap.2819-T1
Valid prediction for GlimmerHMM_glimmerT_35025-T1
Valid prediction for Augustus_model.g23432.t1
Valid prediction for snap_scaffold_14-snap.2815-T1
Couldn't classify 95212, 95440
Sorry, prediction pasa_asmbl_12496.p1 fails validation.
(ATG)	 CC	94285-94490	GT	AGG
(GTT)	 AG	95212-95440	GG	CGG
-recovered pasa_asmbl_12496.p1, initial, 94285, 94490
Valid prediction for HiQ_model.g23424.t1
Valid prediction for GlimmerHMM_glimmerT_35038-T1
Valid prediction for pasa_asmbl_12487.p2
Valid prediction for GlimmerHMM_glimmerT_35031-T1
Valid prediction for snap_scaffold_14-snap.2799-T1
Valid prediction for Augustus_model.g23431.t1
Valid prediction for GlimmerHMM_glimmerT_35040-T1
Valid prediction for GlimmerHMM_glimmerT_35028-T1
Valid prediction for snap_scaffold_14-snap.2825-T1
Valid prediction for snap_scaffold_14-snap.2801-T1
Valid prediction for pasa_asmbl_12482.p1
Valid prediction for GlimmerHMM_glimmerT_35034-T1
Valid prediction for CodingQuarry_transcript_15915-T1
Valid prediction for pasa_asmbl_12751.p1
Valid prediction for snap_scaffold_14-snap.2808-T1
Valid prediction for GlimmerHMM_glimmerT_35026-T1
Valid prediction for snap_scaffold_14-snap.2827-T1
Valid prediction for GlimmerHMM_glimmerT_35042-T1
Valid prediction for GlimmerHMM_glimmerT_35041-T1
Valid prediction for snap_scaffold_14-snap.2816-T1
Valid prediction for Augustus_model.g23425.t1
Valid prediction for GlimmerHMM_glimmerT_35032-T1
Valid prediction for snap_scaffold_14-snap.2805-T1
Valid prediction for snap_scaffold_14-snap.2831-T1
Valid prediction for snap_scaffold_14-snap.2820-T1
Couldn't classify 41588, 41774
Couldn't classify 43515, 43665
Sorry, prediction pasa_asmbl_12492.p1 fails validation.
(GCC)	 TG	41588-41774	GT	AGG
(ACG)	 AG	41925-42177	GT	GGG
(GAT)	 AG	43515-43665	GC	CCG
-recovered pasa_asmbl_12492.p1, internal, 41925, 42177
-recovered pasa_asmbl_12492.p1, internal, 43515, 43665
Valid prediction for Augustus_model.g23433.t1
Valid prediction for snap_scaffold_14-snap.2826-T1
Valid prediction for snap_scaffold_14-snap.2803-T1
Valid prediction for GlimmerHMM_glimmerT_35033-T1
Valid prediction for GlimmerHMM_glimmerT_35024-T1
Valid prediction for Augustus_model.g23435.t1
Valid prediction for snap_scaffold_14-snap.2804-T1
Valid prediction for GlimmerHMM_glimmerT_35022-T1
Valid prediction for HiQ_model.g23417.t1
Valid prediction for HiQ_model.g23429.t1
Couldn't classify 169900, 170052
Couldn't classify 174563, 174693
Sorry, prediction pasa_asmbl_12501.p1 fails validation.
(GCC)	 CT	169900-170052	GT	CTG
(GGC)	 AG	170292-170484	GT	AGG
(GTT)	 AG	173028-173141	GT	GGG
(TGA)	 AG	174563-174693	GT	CGG
-recovered pasa_asmbl_12501.p1, internal, 170292, 170484
-recovered pasa_asmbl_12501.p1, internal, 173028, 173141
-recovered pasa_asmbl_12501.p1, internal, 174563, 174693

-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_14-snap.2823-T1
Valid prediction for Augustus_model.g23418.t1
Couldn't classify 144023, 144250
Sorry, prediction pasa_asmbl_13653.p1 fails validation.
(TGT)	 AG	144023-144250	GT	AGG
(AGA)	 AG	144885-144998	CC	AGC
-recovered pasa_asmbl_13653.p1, terminal, 144885, 144998
-recovered pasa_asmbl_13653.p1, internal, 144023, 144250
Valid prediction for snap_scaffold_14-snap.2812-T1
Valid prediction for HiQ_model.g23416.t1
Valid prediction for snap_scaffold_14-snap.2810-T1
Valid prediction for snap_scaffold_14-snap.2800-T1
Valid prediction for snap_scaffold_14-snap.2828-T1
Valid prediction for GlimmerHMM_glimmerT_35021-T1
Valid prediction for snap_scaffold_14-snap.2824-T1
Valid prediction for HiQ_model.g23428.t1
Valid prediction for CodingQuarry_transcript_15916-T1
Valid prediction for GlimmerHMM_glimmerT_35018-T1
Valid prediction for CodingQuarry_transcript_15914-T1
Valid prediction for snap_scaffold_14-snap.2802-T1
Valid prediction for GlimmerHMM_glimmerT_35015-T1
Valid prediction for snap_scaffold_14-snap.2797-T1
Valid prediction for snap_scaffold_14-snap.2836-T1
Valid prediction for pasa_asmbl_13644.p1
Valid prediction for snap_scaffold_14-snap.2832-T1
Valid prediction for GlimmerHMM_glimmerT_35019-T1
Couldn't classify 187249, 187277
Sorry, prediction pasa_asmbl_13647.p2 fails validation.
(GAG)	 CG	187249-187277	GT	ACG
(ACT)	 AG	187379-187520	GT	AGG
(AGG)	 AG	187887-188151	GT	AGG
(GTG)	 AG	188246-188317	GT	GGG
(GAA)	 AG	188437-188519	AC	AGA
-recovered pasa_asmbl_13647.p2, terminal, 188437, 188519
-recovered pasa_asmbl_13647.p2, internal, 187379, 187520
-recovered pasa_asmbl_13647.p2, internal, 187887, 188151
-recovered pasa_asmbl_13647.p2, internal, 188246, 188317
Valid prediction for GlimmerHMM_glimmerT_35043-T1
Valid prediction for pasa_asmbl_13649.p1
Valid prediction for Augustus_model.g23423.t1
Valid prediction for snap_scaffold_14-snap.2834-T1
Valid prediction for GlimmerHMM_glimmerT_35017-T1
Valid prediction for snap_scaffold_14-snap.2811-T1
Valid prediction for GlimmerHMM_glimmerT_35023-T1
Valid prediction for CodingQuarry_transcript_15919-T1
Couldn't classify 135172, 135372
Sorry, prediction pasa_asmbl_13655.p1 fails validation.
(ATG)	 AG	133642-133878	GT	AGG
(GCT)	 AG	135172-135372	GT	AGG
-recovered pasa_asmbl_13655.p1, initial, 133642, 133878
-recovered pasa_asmbl_13655.p1, internal, 133642, 133878
-recovered pasa_asmbl_13655.p1, internal, 135172, 135372
Valid prediction for snap_scaffold_14-snap.2814-T1
Valid prediction for snap_scaffold_14-snap.2795-T1
Valid prediction for GlimmerHMM_glimmerT_35027-T1
Valid prediction for Augustus_model.g23422.t1
Valid prediction for CodingQuarry_transcript_15913-T1
Valid prediction for snap_scaffold_14-snap.2798-T1
Valid prediction for snap_scaffold_14-snap.2821-T1
Valid prediction for snap_scaffold_14-snap.2806-T1
Valid prediction for pasa_asmbl_13651.p1
Valid prediction for snap_scaffold_14-snap.2835-T1
Valid prediction for HiQ_model.g23420.t1
Valid prediction for GlimmerHMM_glimmerT_35030-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 46979, rend_intergenic: 43545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70903, rend_intergenic: 70140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110736, rend_intergenic: 104043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177125, rend_intergenic: 174579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207094
-exon list size: 350


building trellis

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45.7    
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46.6    
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48.0    
48.3    
48.6    
48.9    
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51.7    
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53.7    
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65.6    
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96.3    
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97.2    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 46979, rend_intergenic: 43545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70903, rend_intergenic: 70140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110736, rend_intergenic: 104043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177125, rend_intergenic: 174579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 190135 - 207094
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 193224 - 207094
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 196905 - 207094