-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_13595659-13881466

-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_4-snap.2841-T1
Valid prediction for GeneMark_model.17498_t
Valid prediction for GeneMark_model.17489_t
Valid prediction for pasa_asmbl_43152.p1
Valid prediction for GeneMark_model.17482_t
Valid prediction for GlimmerHMM_glimmerT_10756-T1
Valid prediction for snap_scaffold_4-snap.2840-T1
Valid prediction for GeneMark_model.17504_t
Valid prediction for GeneMark_model.17462_t
Valid prediction for pasa_asmbl_43144.p1
Couldn't classify 8176, 8272
Sorry, prediction pasa_asmbl_43141.p1 fails validation.
(CTA)	 GT	8176-8272	GT	TGG
(GTA)	 AG	8741-8868	GT	AGG
(TCT)	 AG	9012-9118	GT	GGG
(GGC)	 AG	9236-9366	GT	GGG
(CGT)	 AG	10052-10201	GT	AGG
(TGG)	 AG	10457-10571	GT	AGG
(TGT)	 AG	11102-11180	GT	AGG
(CAG)	 AG	12018-13517	GG	GAG
-recovered pasa_asmbl_43141.p1, terminal, 12018, 13517
-recovered pasa_asmbl_43141.p1, internal, 8741, 8868
-recovered pasa_asmbl_43141.p1, internal, 9012, 9118
-recovered pasa_asmbl_43141.p1, internal, 9236, 9366
-recovered pasa_asmbl_43141.p1, internal, 10052, 10201
-recovered pasa_asmbl_43141.p1, internal, 10457, 10571
-recovered pasa_asmbl_43141.p1, internal, 11102, 11180
Valid prediction for GeneMark_model.17490_t
Valid prediction for snap_scaffold_4-snap.2820-T1
Valid prediction for Augustus_model.g7073.t1
Valid prediction for snap_scaffold_4-snap.2804-T1
Valid prediction for snap_scaffold_4-snap.2808-T1
Valid prediction for GlimmerHMM_glimmerT_10742-T1
Valid prediction for GlimmerHMM_glimmerT_10733-T1
Valid prediction for snap_scaffold_4-snap.2826-T1
Valid prediction for GlimmerHMM_glimmerT_10758-T1
Valid prediction for HiQ_model.g7083.t1
Valid prediction for GeneMark_model.17465_t
Valid prediction for GlimmerHMM_glimmerT_10736-T1
Valid prediction for GeneMark_model.17496_t
Valid prediction for GeneMark_model.17461_t
Valid prediction for CodingQuarry_transcript_49101-T1
Valid prediction for CodingQuarry_transcript_49100-T1
Valid prediction for HiQ_model.g7081.t1
Valid prediction for GeneMark_model.17476_t
Valid prediction for snap_scaffold_4-snap.2836-T1
Valid prediction for GeneMark_model.17475_t
Valid prediction for Augustus_model.g7065.t1
Valid prediction for GlimmerHMM_glimmerT_10744-T1
Valid prediction for snap_scaffold_4-snap.2839-T1
Valid prediction for snap_scaffold_4-snap.2838-T1
Valid prediction for GlimmerHMM_glimmerT_10749-T1
Valid prediction for snap_scaffold_4-snap.2825-T1
Valid prediction for Augustus_model.g7084.t1
Valid prediction for HiQ_model.g7070.t1
Valid prediction for Augustus_model.g7085.t1
Valid prediction for snap_scaffold_4-snap.2810-T1
Valid prediction for snap_scaffold_4-snap.2831-T1
Valid prediction for GeneMark_model.17472_t
Valid prediction for Augustus_model.g7067.t1
Valid prediction for GlimmerHMM_glimmerT_10740-T1
Valid prediction for GeneMark_model.17500_t
Valid prediction for Augustus_model.g7090.t1
Valid prediction for GeneMark_model.17483_t
Valid prediction for snap_scaffold_4-snap.2829-T1
Valid prediction for snap_scaffold_4-snap.2818-T1
Valid prediction for pasa_asmbl_43148.p1
Valid prediction for GeneMark_model.17479_t
Valid prediction for GeneMark_model.17459_t
Couldn't classify 28754, 28838
Couldn't classify 30297, 30360
Sorry, prediction pasa_asmbl_43626.p1 fails validation.
(ATA)	 AG	28754-28838	GT	TGG
(AGA)	 AG	29998-30145	GT	AGG
(TCT)	 AG	30297-30360	CA	CAC
-recovered pasa_asmbl_43626.p1, internal, 28754, 28838
-recovered pasa_asmbl_43626.p1, internal, 29998, 30145
Valid prediction for snap_scaffold_4-snap.2845-T1
Valid prediction for snap_scaffold_4-snap.2806-T1
Valid prediction for snap_scaffold_4-snap.2830-T1
Valid prediction for GeneMark_model.17468_t
Valid prediction for GlimmerHMM_glimmerT_10748-T1
Valid prediction for CodingQuarry_transcript_49094-T1
Valid prediction for Augustus_model.g7063.t1
Couldn't classify 254861, 254908
Sorry, prediction pasa_asmbl_43163.p1 fails validation.
(CAA)	 GT	254861-254908	GT	AGG
(ATA)	 AG	255081-255165	GT	AGG
(GTA)	 AG	255316-255482	GT	AGG
(AAT)	 AG	255579-255692	GT	AGG
(TCG)	 AG	255888-256000	GT	AAG
(GTT)	 AG	256164-256214	GT	AAG
(AGG)	 AG	256371-257154	GA	GAG
-recovered pasa_asmbl_43163.p1, terminal, 256371, 257154
-recovered pasa_asmbl_43163.p1, internal, 255081, 255165
-recovered pasa_asmbl_43163.p1, internal, 255316, 255482
-recovered pasa_asmbl_43163.p1, internal, 255579, 255692
-recovered pasa_asmbl_43163.p1, internal, 255888, 256000
-recovered pasa_asmbl_43163.p1, internal, 256164, 256214
Valid prediction for snap_scaffold_4-snap.2824-T1
Valid prediction for Augustus_model.g7071.t1
Valid prediction for GlimmerHMM_glimmerT_10755-T1
Valid prediction for GlimmerHMM_glimmerT_10753-T1
Valid prediction for snap_scaffold_4-snap.2805-T1
Valid prediction for GeneMark_model.17492_t
Valid prediction for GeneMark_model.17460_t
Valid prediction for Augustus_model.g7072.t1
Valid prediction for GeneMark_model.17470_t
Couldn't classify 149799, 150509
Sorry, prediction pasa_asmbl_43149.p1 fails validation.
(ATG)	 CG	149799-150509	GA	AGG
Valid prediction for GeneMark_model.17484_t
Valid prediction for GeneMark_model.17491_t
Valid prediction for GlimmerHMM_glimmerT_10729-T1
Valid prediction for snap_scaffold_4-snap.2813-T1
Couldn't classify 32384, 32447
Couldn't classify 34811, 35053
Sorry, prediction pasa_asmbl_43143.p1 fails validation.
(CTG)	 GT	32384-32447	GT	AGG
(AGG)	 AG	33454-33626	GT	AGG
(GCT)	 AG	33730-33900	GT	AGG
(AAC)	 AG	34125-34352	GT	TGG
(CTC)	 AG	34811-35053	CT	CCC
-recovered pasa_asmbl_43143.p1, internal, 33454, 33626
-recovered pasa_asmbl_43143.p1, internal, 33730, 33900
-recovered pasa_asmbl_43143.p1, internal, 34125, 34352
Valid prediction for GlimmerHMM_glimmerT_10745-T1
Valid prediction for Augustus_model.g7062.t1
Couldn't classify 211502, 211840
Sorry, prediction pasa_asmbl_43158.p1 fails validation.
(ATG)	 CC	211502-211840	TA	GGT
Valid prediction for snap_scaffold_4-snap.2832-T1
Valid prediction for GlimmerHMM_glimmerT_10741-T1
Valid prediction for HiQ_model.g7078.t1
Valid prediction for snap_scaffold_4-snap.2807-T1
Valid prediction for snap_scaffold_4-snap.2823-T1
Couldn't classify 131262, 131756
Sorry, prediction pasa_asmbl_43561.p2 fails validation.
(TCC)	 GC	131262-131756	AA	GAA
Valid prediction for Augustus_model.g7061.t1
Valid prediction for GlimmerHMM_glimmerT_10752-T1
Valid prediction for snap_scaffold_4-snap.2822-T1
Valid prediction for Augustus_model.g7066.t1
Valid prediction for GlimmerHMM_glimmerT_10731-T1
Valid prediction for GlimmerHMM_glimmerT_10739-T1
Valid prediction for Augustus_model.g7069.t1
Valid prediction for Augustus_model.g7080.t1
Valid prediction for snap_scaffold_4-snap.2811-T1
Valid prediction for GlimmerHMM_glimmerT_10735-T1
Valid prediction for CodingQuarry_transcript_49096-T1
Valid prediction for Augustus_model.g7068.t1
Valid prediction for GlimmerHMM_glimmerT_10743-T1
Valid prediction for GeneMark_model.17467_t
Couldn't classify 265877, 268261
Sorry, prediction pasa_asmbl_43165.p1 fails validation.
(TCT)	 TG	265877-268261	GA	AAG
Valid prediction for HiQ_model.g7079.t1
Valid prediction for snap_scaffold_4-snap.2835-T1
Valid prediction for GlimmerHMM_glimmerT_10751-T1
Valid prediction for snap_scaffold_4-snap.2842-T1
Couldn't classify 222450, 222608
Sorry, prediction pasa_asmbl_43160.p1 fails validation.
(AGG)	 AC	222450-222608	GT	AGG
(TTG)	 AG	222904-223029	GT	AGG
(GGT)	 AG	223205-223375	GT	AGG
(CTG)	 AG	223520-223645	GT	AGG
(CTG)	 AG	223822-224042	GT	AGG
(GCT)	 AG	224284-224587	GT	AGG
(GAC)	 AG	224733-224840	GT	CTG
(ATC)	 AG	224957-225076	GT	AGG
(GAG)	 AG	225246-225302	GT	TGG
(GCG)	 AG	225423-225620	GT	AGG
(GGA)	 AG	225940-225975	AA	AGA
-recovered pasa_asmbl_43160.p1, terminal, 225940, 225975
-recovered pasa_asmbl_43160.p1, internal, 222904, 223029
-recovered pasa_asmbl_43160.p1, internal, 223205, 223375
-recovered pasa_asmbl_43160.p1, internal, 223520, 223645
-recovered pasa_asmbl_43160.p1, internal, 223822, 224042
-recovered pasa_asmbl_43160.p1, internal, 224284, 224587
-recovered pasa_asmbl_43160.p1, internal, 224733, 224840
-recovered pasa_asmbl_43160.p1, internal, 224957, 225076
-recovered pasa_asmbl_43160.p1, internal, 225246, 225302
-recovered pasa_asmbl_43160.p1, internal, 225423, 225620
Valid prediction for Augustus_model.g7091.t1
Valid prediction for snap_scaffold_4-snap.2819-T1
Valid prediction for pasa_asmbl_43154.p1
Valid prediction for Augustus_model.g7074.t1
Valid prediction for HiQ_model.g7088.t1
Valid prediction for GeneMark_model.17501_t
Valid prediction for snap_scaffold_4-snap.2817-T1
Valid prediction for GeneMark_model.17464_t
Valid prediction for GlimmerHMM_glimmerT_10759-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 GlimmerHMM_glimmerT_10734-T1
Valid prediction for GeneMark_model.17494_t
Valid prediction for HiQ_model.g7076.t1
Valid prediction for snap_scaffold_4-snap.2833-T1
Valid prediction for snap_scaffold_4-snap.2837-T1
Valid prediction for GlimmerHMM_glimmerT_10738-T1
Valid prediction for GeneMark_model.17488_t
Valid prediction for snap_scaffold_4-snap.2815-T1
Valid prediction for Augustus_model.g7089.t1
Valid prediction for pasa_asmbl_41748.p1
Valid prediction for GeneMark_model.17477_t
Valid prediction for snap_scaffold_4-snap.2814-T1
Valid prediction for GlimmerHMM_glimmerT_10728-T1
Couldn't classify 47462, 47553
Sorry, prediction pasa_asmbl_42379.p1 fails validation.
(ATG)	 TA	46703-46800	GT	AGG
(TTT)	 AG	46955-47056	GT	AGG
(GGT)	 AG	47156-47256	GT	CCG
(CTC)	 AG	47462-47553	GG	GTG
-recovered pasa_asmbl_42379.p1, initial, 46703, 46800
-recovered pasa_asmbl_42379.p1, internal, 46955, 47056
-recovered pasa_asmbl_42379.p1, internal, 47156, 47256
Valid prediction for GlimmerHMM_glimmerT_10747-T1
Couldn't classify 4311, 4490
Sorry, prediction pasa_asmbl_41763.p1 fails validation.
(GGC)	 CA	4311-4490	GT	TGG
(ACA)	 AG	4838-4858	GT	TGG
(AAT)	 AG	5796-5913	GT	TGG
(AGT)	 AG	6206-6377	GT	GTG
(CAT)	 AG	6768-6836	GT	AGG
(CAT)	 AG	8771-8821	GT	TGG
(GCC)	 AG	10304-10730	AG	AAA
-recovered pasa_asmbl_41763.p1, terminal, 10304, 10730
-recovered pasa_asmbl_41763.p1, internal, 4838, 4858
-recovered pasa_asmbl_41763.p1, internal, 5796, 5913
-recovered pasa_asmbl_41763.p1, internal, 6206, 6377
-recovered pasa_asmbl_41763.p1, internal, 6768, 6836
-recovered pasa_asmbl_41763.p1, internal, 8771, 8821
Valid prediction for snap_scaffold_4-snap.2816-T1
Valid prediction for CodingQuarry_transcript_49099-T1
Valid prediction for GeneMark_model.17474_t
Valid prediction for GeneMark_model.17463_t
Valid prediction for snap_scaffold_4-snap.2843-T1
Valid prediction for snap_scaffold_4-snap.2834-T1
Valid prediction for CodingQuarry_transcript_49104-T1
Valid prediction for GeneMark_model.17487_t
Valid prediction for Augustus_model.g7086.t1
Valid prediction for CodingQuarry_transcript_49102-T1
Valid prediction for Augustus_model.g7064.t1
Valid prediction for GlimmerHMM_glimmerT_10746-T1
Valid prediction for GeneMark_model.17478_t
Valid prediction for snap_scaffold_4-snap.2809-T1
Valid prediction for Augustus_model.g7082.t1
Valid prediction for Augustus_model.g7087.t1
Valid prediction for snap_scaffold_4-snap.2828-T1
Couldn't classify 52869, 53033
Sorry, prediction pasa_asmbl_41756.p1 fails validation.
(GGG)	 CA	52869-53033	GT	CGG
(ATG)	 AG	53471-53573	GT	GGG
(GTT)	 AG	53776-53922	GT	GAG
(TCT)	 AG	54035-54166	GT	CGG
(AAT)	 AG	54338-54466	GT	ACG
(AGT)	 AG	54687-54812	GT	AGG
(AGC)	 AG	55062-55271	GT	AGG
(ATG)	 AG	55357-55466	GT	AGG
(AAC)	 AG	55627-55753	GT	AGG
(GAG)	 AG	55931-55993	GT	AGG
(AGC)	 AG	56204-56398	GT	AGG
(AAC)	 AG	57101-57243	CA	GAC
-recovered pasa_asmbl_41756.p1, initial, 53471, 53573
-recovered pasa_asmbl_41756.p1, initial, 55357, 55466
-recovered pasa_asmbl_41756.p1, terminal, 57101, 57243
-recovered pasa_asmbl_41756.p1, internal, 53471, 53573
-recovered pasa_asmbl_41756.p1, internal, 53776, 53922
-recovered pasa_asmbl_41756.p1, internal, 54035, 54166
-recovered pasa_asmbl_41756.p1, internal, 54338, 54466
-recovered pasa_asmbl_41756.p1, internal, 54687, 54812
-recovered pasa_asmbl_41756.p1, internal, 55062, 55271
-recovered pasa_asmbl_41756.p1, internal, 55357, 55466
-recovered pasa_asmbl_41756.p1, internal, 55627, 55753
-recovered pasa_asmbl_41756.p1, internal, 55931, 55993
-recovered pasa_asmbl_41756.p1, internal, 56204, 56398
Valid prediction for snap_scaffold_4-snap.2803-T1
Valid prediction for GeneMark_model.17502_t
Valid prediction for GeneMark_model.17469_t
Valid prediction for GeneMark_model.17493_t
Valid prediction for snap_scaffold_4-snap.2827-T1
Valid prediction for GeneMark_model.17481_t
Valid prediction for GeneMark_model.17505_t
Valid prediction for snap_scaffold_4-snap.2821-T1
Valid prediction for GlimmerHMM_glimmerT_10730-T1
Valid prediction for GeneMark_model.17466_t
Valid prediction for GlimmerHMM_glimmerT_10737-T1
Valid prediction for Augustus_model.g7075.t1
Valid prediction for Augustus_model.g7077.t1
Valid prediction for GeneMark_model.17486_t
Valid prediction for GlimmerHMM_glimmerT_10757-T1
Valid prediction for GeneMark_model.17497_t
Valid prediction for GeneMark_model.17499_t
Valid prediction for GlimmerHMM_glimmerT_10754-T1
Couldn't classify 50662, 50909
Couldn't classify 52595, 52675
Sorry, prediction pasa_asmbl_41760.p1 fails validation.
(GCC)	 CA	50662-50909	GT	CTG
(TTG)	 AG	51515-51620	GT	CGG
(GGT)	 AG	51709-51845	GT	AGG
(GTG)	 AG	51962-52174	GT	AGG
(CTG)	 AG	52306-52480	GT	CGG
(GGG)	 AG	52595-52675	GA	TGG
-recovered pasa_asmbl_41760.p1, internal, 51515, 51620
-recovered pasa_asmbl_41760.p1, internal, 51709, 51845
-recovered pasa_asmbl_41760.p1, internal, 51962, 52174
-recovered pasa_asmbl_41760.p1, internal, 52306, 52480
Valid prediction for GlimmerHMM_glimmerT_10750-T1
Valid prediction for GeneMark_model.17471_t
Valid prediction for GlimmerHMM_glimmerT_10732-T1
Valid prediction for Augustus_model.g7092.t1
Valid prediction for snap_scaffold_4-snap.2812-T1
Valid prediction for GeneMark_model.17503_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 235845, rend_intergenic: 235167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 285808
-exon list size: 525


building trellis

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64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 235845, rend_intergenic: 235167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support