-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_15003344-15216504

-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 GeneMark_model.65714_t
Valid prediction for snap_scaffold_15-snap.3009-T1
Valid prediction for GlimmerHMM_glimmerT_38261-T1
Valid prediction for GeneMark_model.65713_t
Valid prediction for GeneMark_model.65715_t
Valid prediction for GeneMark_model.65728_t
Couldn't classify 105323, 105448
Sorry, prediction pasa_asmbl_14661.p1 fails validation.
(TGG)	 GG	105323-105448	GT	TGG
(GAT)	 AG	105554-105583	GT	AAG
(GTG)	 AG	105790-105902	GT	AGG
(CTG)	 AG	106297-106429	GT	TTG
(GAG)	 AG	106725-106864	GT	ATG
(GTG)	 AG	108119-108242	GT	AGG
(AAA)	 AG	108333-108491	GT	AGG
(CTA)	 AG	109054-109219	GT	AGG
(GAG)	 AG	109434-109522	GG	GAG
-recovered pasa_asmbl_14661.p1, terminal, 109434, 109522
-recovered pasa_asmbl_14661.p1, internal, 105554, 105583
-recovered pasa_asmbl_14661.p1, internal, 105790, 105902
-recovered pasa_asmbl_14661.p1, internal, 106297, 106429
-recovered pasa_asmbl_14661.p1, internal, 106725, 106864
-recovered pasa_asmbl_14661.p1, internal, 108119, 108242
-recovered pasa_asmbl_14661.p1, internal, 108333, 108491
-recovered pasa_asmbl_14661.p1, internal, 109054, 109219
Valid prediction for GeneMark_model.65725_t
Valid prediction for snap_scaffold_15-snap.3023-T1
Valid prediction for HiQ_model.g25686.t1
Valid prediction for GeneMark_model.65734_t
Valid prediction for CodingQuarry_transcript_18207-T1
Valid prediction for GlimmerHMM_glimmerT_38270-T1
Valid prediction for snap_scaffold_15-snap.3024-T1
Valid prediction for snap_scaffold_15-snap.3004-T1
Valid prediction for GeneMark_model.65724_t
Valid prediction for GeneMark_model.65737_t
Couldn't classify 168145, 168232
Sorry, prediction pasa_asmbl_14670.p1 fails validation.
(ATG)	 CC	160252-160350	GT	TGG
(GAT)	 AG	162605-162686	GT	ATG
(ATG)	 AG	163198-163298	GT	TAG
(GTC)	 AG	163639-163776	GT	AGG
(CTT)	 AG	163896-164156	GT	CAG
(ACA)	 AG	165944-166088	GT	CGG
(GTG)	 AG	166313-166451	GT	AGG
(GGA)	 AG	168145-168232	GA	GAG
-recovered pasa_asmbl_14670.p1, initial, 160252, 160350
add_exon() Sorry, pasa_asmbl_14670.p1 163198-163298-initial-1 is invalid.
-recovered pasa_asmbl_14670.p1, initial, 163198, 163298
-recovered pasa_asmbl_14670.p1, internal, 162605, 162686
-recovered pasa_asmbl_14670.p1, internal, 163198, 163298
-recovered pasa_asmbl_14670.p1, internal, 163639, 163776
-recovered pasa_asmbl_14670.p1, internal, 163896, 164156
-recovered pasa_asmbl_14670.p1, internal, 165944, 166088
-recovered pasa_asmbl_14670.p1, internal, 166313, 166451
Valid prediction for Augustus_model.g25676.t1
Valid prediction for snap_scaffold_15-snap.3019-T1
Valid prediction for Augustus_model.g25683.t1
Valid prediction for GeneMark_model.65736_t
Valid prediction for GeneMark_model.65732_t
Valid prediction for snap_scaffold_15-snap.3007-T1
Valid prediction for GlimmerHMM_glimmerT_38272-T1
Couldn't classify 171346, 171503
Sorry, prediction pasa_asmbl_14688.p1 fails validation.
(GTG)	 CT	171346-171503	GT	GAG
(GCT)	 AG	172122-172215	GC	AGG
(CCT)	 AG	172422-172507	GT	AGG
(AAA)	 AG	173379-173427	GC	AGG
(ATG)	 AG	173536-173671	GT	AGG
(TCA)	 AG	173913-174004	GT	AGG
(CTG)	 AG	174203-174449	GT	GGG
(GGC)	 AG	175594-175700	GT	GAG
(GAG)	 AG	176039-176198	GT	AGG
(CGA)	 AG	176359-176519	GT	AGG
(ACG)	 AG	176700-176884	GT	AGG
(GGA)	 AG	177117-177186	GT	CGG
(ACC)	 AG	177417-177520	GT	AGG
(GGA)	 AG	178623-178809	GT	CTG
(CTG)	 AG	179408-179501	GT	GCG
(AGC)	 AG	179697-179791	GT	AGG
(GCT)	 AG	180240-180434	GT	CGG
(TTG)	 AG	181077-181245	GT	AGG
(ATG)	 AG	182128-182195	GT	AGG
(TAC)	 AG	182296-182384	GT	GAG
(TAA)	 AG	182717-182795	GT	AGG
(ATC)	 AG	183506-183773	GT	AGG
(TGA)	 AG	184465-184735	GT	AGG
(GTT)	 AG	185786-185861	AG	AAA
-recovered pasa_asmbl_14688.p1, initial, 173536, 173671
-recovered pasa_asmbl_14688.p1, initial, 182128, 182195
add_exon() Sorry, pasa_asmbl_14688.p1 182296-182384-terminal-2 is invalid.
-recovered pasa_asmbl_14688.p1, terminal, 182296, 182384
-recovered pasa_asmbl_14688.p1, terminal, 185786, 185861
-recovered pasa_asmbl_14688.p1, internal, 172122, 172215
-recovered pasa_asmbl_14688.p1, internal, 172422, 172507
-recovered pasa_asmbl_14688.p1, internal, 173379, 173427
-recovered pasa_asmbl_14688.p1, internal, 173536, 173671
-recovered pasa_asmbl_14688.p1, internal, 173913, 174004
-recovered pasa_asmbl_14688.p1, internal, 174203, 174449
-recovered pasa_asmbl_14688.p1, internal, 175594, 175700
-recovered pasa_asmbl_14688.p1, internal, 176039, 176198
-recovered pasa_asmbl_14688.p1, internal, 176359, 176519
-recovered pasa_asmbl_14688.p1, internal, 176700, 176884
-recovered pasa_asmbl_14688.p1, internal, 177117, 177186
-recovered pasa_asmbl_14688.p1, internal, 177417, 177520
-recovered pasa_asmbl_14688.p1, internal, 178623, 178809
-recovered pasa_asmbl_14688.p1, internal, 179408, 179501
-recovered pasa_asmbl_14688.p1, internal, 179697, 179791
-recovered pasa_asmbl_14688.p1, internal, 180240, 180434
-recovered pasa_asmbl_14688.p1, internal, 181077, 181245
-recovered pasa_asmbl_14688.p1, internal, 182128, 182195
-recovered pasa_asmbl_14688.p1, internal, 182296, 182384
-recovered pasa_asmbl_14688.p1, internal, 182717, 182795
-recovered pasa_asmbl_14688.p1, internal, 183506, 183773
-recovered pasa_asmbl_14688.p1, internal, 184465, 184735
Valid prediction for snap_scaffold_15-snap.3021-T1
Valid prediction for snap_scaffold_15-snap.3027-T1
Valid prediction for Augustus_model.g25677.t1
Valid prediction for GlimmerHMM_glimmerT_38278-T1
Couldn't classify 103321, 103350
Couldn't classify 105790, 105840
Sorry, prediction pasa_asmbl_14812.p1 fails validation.
(CAT)	 AG	103321-103350	GT	CTG
(GAT)	 AG	103806-103951	GT	GTG
(GTG)	 AG	105322-105448	GT	TGG
(GAT)	 AG	105554-105583	GT	AAG
(GTG)	 AG	105790-105840	GA	AGG
-recovered pasa_asmbl_14812.p1, internal, 103321, 103350
-recovered pasa_asmbl_14812.p1, internal, 103806, 103951
-recovered pasa_asmbl_14812.p1, internal, 105322, 105448
-recovered pasa_asmbl_14812.p1, internal, 105554, 105583
Valid prediction for GeneMark_model.65721_t
Valid prediction for GlimmerHMM_glimmerT_38276-T1
Valid prediction for GlimmerHMM_glimmerT_38279-T1
Valid prediction for Augustus_model.g25680.t1
Valid prediction for snap_scaffold_15-snap.3005-T1
Valid prediction for GlimmerHMM_glimmerT_38280-T1
Valid prediction for GlimmerHMM_glimmerT_38263-T1
Valid prediction for CodingQuarry_transcript_18204-T1
Valid prediction for snap_scaffold_15-snap.3006-T1
Valid prediction for snap_scaffold_15-snap.3018-T1
Valid prediction for GlimmerHMM_glimmerT_38275-T1
Valid prediction for pasa_asmbl_14669.p1
Valid prediction for GeneMark_model.65722_t
Valid prediction for Augustus_model.g25688.t1
Valid prediction for snap_scaffold_15-snap.3008-T1
Valid prediction for snap_scaffold_15-snap.2997-T1
Valid prediction for GlimmerHMM_glimmerT_38268-T1
Valid prediction for CodingQuarry_transcript_18209-T1
Valid prediction for GeneMark_model.65716_t
Valid prediction for snap_scaffold_15-snap.3029-T1
Valid prediction for GlimmerHMM_glimmerT_38274-T1
Valid prediction for snap_scaffold_15-snap.2993-T1
Valid prediction for GlimmerHMM_glimmerT_38266-T1
Valid prediction for GeneMark_model.65720_t
Valid prediction for snap_scaffold_15-snap.3015-T1
Valid prediction for snap_scaffold_15-snap.3026-T1
Valid prediction for GlimmerHMM_glimmerT_38283-T1
Valid prediction for GeneMark_model.65738_t
Valid prediction for snap_scaffold_15-snap.3017-T1
Valid prediction for GeneMark_model.65733_t
Valid prediction for GlimmerHMM_glimmerT_38282-T1
Valid prediction for GlimmerHMM_glimmerT_38281-T1
Valid prediction for GlimmerHMM_glimmerT_38260-T1
Valid prediction for snap_scaffold_15-snap.3025-T1
Valid prediction for GeneMark_model.65735_t
Valid prediction for Augustus_model.g25684.t1
Valid prediction for snap_scaffold_15-snap.3003-T1
Valid prediction for GeneMark_model.65740_t
Valid prediction for snap_scaffold_15-snap.3022-T1
Valid prediction for Augustus_model.g25669.t1
Valid prediction for GlimmerHMM_glimmerT_38262-T1
Valid prediction for Augustus_model.g25678.t1
Valid prediction for GlimmerHMM_glimmerT_38286-T1
Valid prediction for HiQ_model.g25685.t1
Valid prediction for Augustus_model.g25672.t1
Valid prediction for CodingQuarry_transcript_18206-T1
Valid prediction for snap_scaffold_15-snap.2991-T1
Couldn't classify 97247, 97303
Couldn't classify 102880, 102936
Sorry, prediction pasa_asmbl_14660.p1 fails validation.
(CCC)	 TC	97247-97303	GT	AGG
(AAG)	 AG	97926-98093	GT	ACG
(ATG)	 AG	98376-98414	GT	AGG
(ATG)	 AG	98924-99042	GT	TGG
(CTG)	 AG	99441-99600	GT	GTG
(GAC)	 AG	99856-99995	GT	GTG
(GTG)	 AG	101220-101346	GT	TGG
(GGT)	 AG	101957-101992	GT	AGG
(GCT)	 AG	102880-102936	GT	ATG
-recovered pasa_asmbl_14660.p1, initial, 98376, 98414
-recovered pasa_asmbl_14660.p1, initial, 98924, 99042
-recovered pasa_asmbl_14660.p1, internal, 97926, 98093
-recovered pasa_asmbl_14660.p1, internal, 98376, 98414
-recovered pasa_asmbl_14660.p1, internal, 98924, 99042
-recovered pasa_asmbl_14660.p1, internal, 99441, 99600
-recovered pasa_asmbl_14660.p1, internal, 99856, 99995
-recovered pasa_asmbl_14660.p1, internal, 101220, 101346
-recovered pasa_asmbl_14660.p1, internal, 101957, 101992
-recovered pasa_asmbl_14660.p1, internal, 102880, 102936
Valid prediction for GlimmerHMM_glimmerT_38284-T1
Valid prediction for Augustus_model.g25673.t1
Valid prediction for CodingQuarry_transcript_18208-T1
Valid prediction for pasa_asmbl_14682.p1
Valid prediction for Augustus_model.g25690.t1
Valid prediction for snap_scaffold_15-snap.3001-T1
Valid prediction for CodingQuarry_transcript_18205-T1
Valid prediction for GeneMark_model.65726_t

-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.65723_t
Valid prediction for GeneMark_model.65717_t
Couldn't classify 85650, 85677
Sorry, prediction pasa_asmbl_15775.p1 fails validation.
(AGA)	 GG	85650-85677	GT	AGG
(GAG)	 AG	86474-86628	GT	AGG
(GTG)	 AG	86743-86811	GT	AGG
(GTC)	 AG	88851-88975	GT	CGG
(GTC)	 AG	89617-89629	CA	AGC
-recovered pasa_asmbl_15775.p1, terminal, 89617, 89629
-recovered pasa_asmbl_15775.p1, internal, 86474, 86628
-recovered pasa_asmbl_15775.p1, internal, 86743, 86811
-recovered pasa_asmbl_15775.p1, internal, 88851, 88975
Valid prediction for snap_scaffold_15-snap.3016-T1
Valid prediction for GlimmerHMM_glimmerT_38271-T1
Valid prediction for GlimmerHMM_glimmerT_38264-T1
Couldn't classify 93123, 93149
Sorry, prediction pasa_asmbl_15771.p1 fails validation.
(GGA)	 CA	93123-93149	GT	AGG
(TTA)	 AG	95313-95449	GT	AAG
(GTT)	 AG	96578-96761	GT	AGG
(AAC)	 AG	99077-99172	GT	AGG
(ATC)	 AG	100197-100379	TG	GAT
-recovered pasa_asmbl_15771.p1, terminal, 100197, 100379
-recovered pasa_asmbl_15771.p1, internal, 95313, 95449
-recovered pasa_asmbl_15771.p1, internal, 96578, 96761
-recovered pasa_asmbl_15771.p1, internal, 99077, 99172
Valid prediction for snap_scaffold_15-snap.2996-T1
Valid prediction for GlimmerHMM_glimmerT_38267-T1
Valid prediction for CodingQuarry_transcript_18203-T1
Valid prediction for Augustus_model.g25671.t1
Valid prediction for Augustus_model.g25687.t1
Valid prediction for GlimmerHMM_glimmerT_38265-T1
Valid prediction for CodingQuarry_transcript_18210-T1
Valid prediction for HiQ_model.g25689.t1
Valid prediction for GeneMark_model.65739_t
Valid prediction for Augustus_model.g25670.t1
Valid prediction for pasa_asmbl_15777.p1
Valid prediction for snap_scaffold_15-snap.3002-T1
Valid prediction for GlimmerHMM_glimmerT_38269-T1
Valid prediction for GeneMark_model.65719_t
Valid prediction for GeneMark_model.65712_t
Valid prediction for GlimmerHMM_glimmerT_38285-T1
Valid prediction for HiQ_model.g25682.t1
Valid prediction for snap_scaffold_15-snap.3012-T1
Valid prediction for snap_scaffold_15-snap.3013-T1
Valid prediction for Augustus_model.g25681.t1
Valid prediction for GeneMark_model.65742_t
Valid prediction for GeneMark_model.65730_t
Valid prediction for Augustus_model.g25674.t1
Valid prediction for snap_scaffold_15-snap.2992-T1
Valid prediction for snap_scaffold_15-snap.3010-T1
Valid prediction for snap_scaffold_15-snap.3020-T1
Valid prediction for snap_scaffold_15-snap.2990-T1
Valid prediction for snap_scaffold_15-snap.3011-T1
Valid prediction for CodingQuarry_transcript_18202-T1
Valid prediction for snap_scaffold_15-snap.2999-T1
Valid prediction for snap_scaffold_15-snap.2995-T1
Valid prediction for GeneMark_model.65741_t
Valid prediction for snap_scaffold_15-snap.3028-T1
Valid prediction for snap_scaffold_15-snap.2994-T1
Valid prediction for GlimmerHMM_glimmerT_38277-T1
Valid prediction for snap_scaffold_15-snap.2998-T1
Valid prediction for GlimmerHMM_glimmerT_38273-T1
Valid prediction for GeneMark_model.65718_t
Valid prediction for snap_scaffold_15-snap.3000-T1
Valid prediction for GeneMark_model.65731_t
Valid prediction for Augustus_model.g25679.t1
Valid prediction for snap_scaffold_15-snap.3014-T1
Valid prediction for Augustus_model.g25675.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28312, rend_intergenic: 25786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154725, rend_intergenic: 151428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155973, rend_intergenic: 154729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213161
-exon list size: 449


building trellis

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82.9    
83.1    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.0    
90.2    
90.5    
90.7    
90.9    
91.1    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 28312, rend_intergenic: 25786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154725, rend_intergenic: 151428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155973, rend_intergenic: 154729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support