-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_4016785-4159479

-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 CodingQuarry_transcript_40308-T1
Valid prediction for Augustus_model.g36740.t1
Valid prediction for CodingQuarry_transcript_40309-T1
Couldn't classify 64261, 64362
Couldn't classify 67832, 68044
Sorry, prediction pasa_asmbl_34852.p1 fails validation.
(CCA)	 AG	64261-64362	GT	AGG
(ATC)	 AG	65183-65222	GT	GGG
(GGC)	 AG	65347-65612	GT	AAG
(CCT)	 AG	65717-65800	GT	AGG
(GTG)	 AG	66861-66972	GT	TGG
(TTC)	 AG	67420-67463	GT	AGG
(AGG)	 AG	67609-67731	GT	AGG
(GAG)	 AG	67832-68044	CC	CCC
-recovered pasa_asmbl_34852.p1, internal, 64261, 64362
-recovered pasa_asmbl_34852.p1, internal, 65183, 65222
-recovered pasa_asmbl_34852.p1, internal, 65347, 65612
-recovered pasa_asmbl_34852.p1, internal, 65717, 65800
-recovered pasa_asmbl_34852.p1, internal, 66861, 66972
-recovered pasa_asmbl_34852.p1, internal, 67420, 67463
-recovered pasa_asmbl_34852.p1, internal, 67609, 67731
Valid prediction for GlimmerHMM_glimmerT_55460-T1
Valid prediction for snap_scaffold_26-snap.869-T1
Valid prediction for CodingQuarry_transcript_40312-T1
Valid prediction for snap_scaffold_26-snap.883-T1
Couldn't classify 137332, 137382
Sorry, prediction pasa_asmbl_34876.p1 fails validation.
(ATG)	 AC	136416-136670	GT	GGG
(GTC)	 AG	136799-136978	GT	AGG
(AAT)	 AG	137332-137382	AA	CCA
-recovered pasa_asmbl_34876.p1, initial, 136416, 136670
-recovered pasa_asmbl_34876.p1, internal, 136799, 136978
Valid prediction for GlimmerHMM_glimmerT_55449-T1
Valid prediction for Augustus_model.g36739.t1
Valid prediction for GlimmerHMM_glimmerT_55465-T1
Valid prediction for GlimmerHMM_glimmerT_55468-T1
Couldn't classify 68570, 68740
Sorry, prediction pasa_asmbl_34854.p1 fails validation.
(CGC)	 CA	68570-68740	GT	CGG
(GAA)	 AG	68945-69015	GT	CTG
(GGC)	 AG	69394-69495	GT	AGG
(GCC)	 AG	69602-69663	GT	ACG
(TCG)	 AG	69795-69961	GT	AGG
(GTG)	 AG	70077-70310	AG	AAA
-recovered pasa_asmbl_34854.p1, terminal, 70077, 70310
-recovered pasa_asmbl_34854.p1, internal, 68945, 69015
-recovered pasa_asmbl_34854.p1, internal, 69394, 69495
-recovered pasa_asmbl_34854.p1, internal, 69602, 69663
-recovered pasa_asmbl_34854.p1, internal, 69795, 69961
Valid prediction for GlimmerHMM_glimmerT_55451-T1
Valid prediction for pasa_asmbl_34859.p1
Valid prediction for GlimmerHMM_glimmerT_55459-T1
Valid prediction for GlimmerHMM_glimmerT_55452-T1
Valid prediction for snap_scaffold_26-snap.855-T1
Couldn't classify 130156, 130455
Sorry, prediction pasa_asmbl_34875.p2 fails validation.
(ATG)	 GG	129952-129960	GT	AGG
(ACC)	 AG	130156-130455	CT	ACC
-recovered pasa_asmbl_34875.p2, initial, 129952, 129960
Valid prediction for snap_scaffold_26-snap.893-T1
Valid prediction for snap_scaffold_26-snap.859-T1
Valid prediction for snap_scaffold_26-snap.881-T1
Valid prediction for pasa_asmbl_34864.p1
Couldn't classify 82512, 82593
Couldn't classify 84565, 84592
Sorry, prediction pasa_asmbl_34855.p1 fails validation.
(CTT)	 GG	82512-82593	GT	AGG
(ACT)	 AG	83709-83809	GT	GAG
(TAC)	 AG	83906-83954	GT	AGG
(GGG)	 AG	84327-84432	GT	AGG
(CTC)	 AG	84565-84592	CA	GTC
-recovered pasa_asmbl_34855.p1, internal, 83709, 83809
-recovered pasa_asmbl_34855.p1, internal, 83906, 83954
-recovered pasa_asmbl_34855.p1, internal, 84327, 84432
Valid prediction for snap_scaffold_26-snap.871-T1
Valid prediction for HiQ_model.g36738.t1
Valid prediction for HiQ_model.g36742.t1
Valid prediction for snap_scaffold_26-snap.880-T1
Couldn't classify 86570, 86750
Couldn't classify 86984, 87171
Sorry, prediction pasa_asmbl_34857.p1 fails validation.
(GAG)	 AG	86570-86750	GT	AGG
(GGT)	 AG	86984-87171	GA	GAG
-recovered pasa_asmbl_34857.p1, internal, 86570, 86750
Valid prediction for snap_scaffold_26-snap.867-T1
Couldn't classify 113838, 113878
Sorry, prediction pasa_asmbl_34869.p1 fails validation.
(CTG)	 CC	113838-113878	GT	TGG
(CTT)	 AG	114767-114830	GT	AGG
(AGG)	 AG	115282-115494	AG	GAA
-recovered pasa_asmbl_34869.p1, terminal, 115282, 115494
-recovered pasa_asmbl_34869.p1, internal, 114767, 114830
Valid prediction for HiQ_model.g36737.t1
Valid prediction for HiQ_model.g36736.t1
Valid prediction for snap_scaffold_26-snap.854-T1
Valid prediction for GlimmerHMM_glimmerT_55469-T1
Valid prediction for snap_scaffold_26-snap.888-T1
Valid prediction for Augustus_model.g36728.t1
Valid prediction for GlimmerHMM_glimmerT_55446-T1
Valid prediction for snap_scaffold_26-snap.884-T1
Valid prediction for Augustus_model.g36735.t1
Valid prediction for Augustus_model.g36730.t1
Valid prediction for CodingQuarry_transcript_40311-T1
Couldn't classify 109264, 109782
Sorry, prediction pasa_asmbl_34867.p1 fails validation.
(CGG)	 GT	109264-109782	GG	AAG
Couldn't classify 3732, 3795
Couldn't classify 7512, 7580
Sorry, prediction pasa_asmbl_34848.p1 fails validation.
(TTC)	 AC	3732-3795	GT	AGG
(GTG)	 AG	5519-5580	GT	AGG
(AGA)	 AG	5717-5776	GT	TGG
(AAA)	 AG	5934-6048	GT	AGG
(GTC)	 AG	6225-6367	GT	AGG
(ATC)	 AG	6841-6966	GT	AGG
(ATC)	 AG	7512-7580	AA	TCA
-recovered pasa_asmbl_34848.p1, internal, 5519, 5580
-recovered pasa_asmbl_34848.p1, internal, 5717, 5776
-recovered pasa_asmbl_34848.p1, internal, 5934, 6048
-recovered pasa_asmbl_34848.p1, internal, 6225, 6367
-recovered pasa_asmbl_34848.p1, internal, 6841, 6966
Valid prediction for snap_scaffold_26-snap.865-T1
Valid prediction for GlimmerHMM_glimmerT_55458-T1
Valid prediction for GlimmerHMM_glimmerT_55450-T1
Valid prediction for GlimmerHMM_glimmerT_55461-T1
Valid prediction for Augustus_model.g36729.t1
Valid prediction for Augustus_model.g36743.t1
Valid prediction for snap_scaffold_26-snap.874-T1
Valid prediction for GlimmerHMM_glimmerT_55454-T1
Couldn't classify 85524, 85682
Sorry, prediction pasa_asmbl_34856.p1 fails validation.
(ATG)	 TG	84766-84896	GT	GTG
(ACG)	 AG	85022-85168	GT	AAG
(CTC)	 AG	85250-85379	GT	AGG
(CTG)	 AG	85524-85682	CA	CAC
-recovered pasa_asmbl_34856.p1, initial, 84766, 84896
-recovered pasa_asmbl_34856.p1, internal, 85022, 85168
-recovered pasa_asmbl_34856.p1, internal, 85250, 85379
Valid prediction for snap_scaffold_26-snap.889-T1
Valid prediction for HiQ_model.g36731.t1
Valid prediction for pasa_asmbl_34871.p1
Valid prediction for snap_scaffold_26-snap.891-T1
Valid prediction for snap_scaffold_26-snap.895-T1
Valid prediction for CodingQuarry_transcript_40305-T1
Valid prediction for snap_scaffold_26-snap.875-T1
Valid prediction for Augustus_model.g36744.t1
Valid prediction for CodingQuarry_transcript_40310-T1
Valid prediction for snap_scaffold_26-snap.894-T1
Valid prediction for GlimmerHMM_glimmerT_55453-T1
Valid prediction for CodingQuarry_transcript_40303-T1
Valid prediction for snap_scaffold_26-snap.882-T1
Valid prediction for CodingQuarry_transcript_40304-T1
Valid prediction for GlimmerHMM_glimmerT_55447-T1
Valid prediction for GlimmerHMM_glimmerT_55462-T1
Valid prediction for snap_scaffold_26-snap.890-T1
Couldn't classify 64005, 64146
Sorry, prediction pasa_asmbl_34851.p3 fails validation.
(ATG)	 GC	61926-61979	GT	AGG
(GTG)	 AG	63575-63762	GT	AGG
(GAA)	 AG	64005-64146	AC	AGA
-recovered pasa_asmbl_34851.p3, initial, 61926, 61979
-recovered pasa_asmbl_34851.p3, internal, 63575, 63762
Valid prediction for pasa_asmbl_34863.p1
Valid prediction for GlimmerHMM_glimmerT_55467-T1
Couldn't classify 15678, 15792
Couldn't classify 19867, 19911
Sorry, prediction pasa_asmbl_34849.p1 fails validation.
(AGG)	 CC	15678-15792	GT	TGG
(GTA)	 AG	16164-16319	GT	CGG
(ATG)	 AG	16637-17020	GT	ACG
(CCA)	 AG	17176-17337	GT	CAG
(ATA)	 AG	17787-17915	GT	AGG
(CAC)	 AG	18336-18422	GT	AGG
(GCT)	 AG	18610-18849	GT	CGG
(GTC)	 AG	19287-19435	GT	AGG
(ATC)	 AG	19549-19725	GT	AGG
(GCG)	 AG	19867-19911	GA	TGG
add_exon() Sorry, pasa_asmbl_34849.p1 16637-17020-initial-1 is invalid.
-recovered pasa_asmbl_34849.p1, initial, 16637, 17020
-recovered pasa_asmbl_34849.p1, internal, 16164, 16319
-recovered pasa_asmbl_34849.p1, internal, 16637, 17020
-recovered pasa_asmbl_34849.p1, internal, 17176, 17337
-recovered pasa_asmbl_34849.p1, internal, 17787, 17915
-recovered pasa_asmbl_34849.p1, internal, 18336, 18422
-recovered pasa_asmbl_34849.p1, internal, 18610, 18849
-recovered pasa_asmbl_34849.p1, internal, 19287, 19435
-recovered pasa_asmbl_34849.p1, internal, 19549, 19725
Couldn't classify 105158, 105279
Couldn't classify 106819, 106961
Sorry, prediction pasa_asmbl_34866.p1 fails validation.
(AAC)	 GG	105158-105279	GT	AGG
(GCA)	 AG	105397-105491	GT	TGG
(ATC)	 AG	105643-105688	GT	AGG
(CAG)	 AG	106093-106144	GT	CGG
(CTC)	 AG	106227-106299	GT	AGG
(TTT)	 AG	106434-106531	GC	AGG
(GGA)	 AG	106669-106780	GT	AGG
(ATA)	 AG	106819-106961	GT	AGG
-recovered pasa_asmbl_34866.p1, internal, 105397, 105491
-recovered pasa_asmbl_34866.p1, internal, 105643, 105688
-recovered pasa_asmbl_34866.p1, internal, 106093, 106144
-recovered pasa_asmbl_34866.p1, internal, 106227, 106299
-recovered pasa_asmbl_34866.p1, internal, 106434, 106531
-recovered pasa_asmbl_34866.p1, internal, 106669, 106780
-recovered pasa_asmbl_34866.p1, internal, 106819, 106961
Valid prediction for GlimmerHMM_glimmerT_55448-T1
Valid prediction for GlimmerHMM_glimmerT_55463-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_26-snap.887-T1
Valid prediction for Augustus_model.g36733.t1
Valid prediction for GlimmerHMM_glimmerT_55466-T1
Couldn't classify 21234, 21316
Sorry, prediction pasa_asmbl_35531.p1 fails validation.
(GAG)	 AA	21234-21316	GT	AGG
(CAT)	 AG	21452-21662	GT	GAG
(CTT)	 AG	21889-21945	GT	AGG
(ATG)	 AG	22524-22592	GT	AGG
(CAA)	 AG	22942-23115	GT	AGG
(GCC)	 AG	23364-23476	GT	GGG
(GCG)	 AG	23558-23624	GT	TGG
(GAG)	 AG	23732-23904	GT	AGG
(GGA)	 AG	24037-24118	GT	AGG
(GTC)	 AG	24238-24423	GT	AGG
(GTG)	 AG	24518-24661	GT	AGG
(GTT)	 AG	25027-25059	AG	AGA
-recovered pasa_asmbl_35531.p1, initial, 22524, 22592
-recovered pasa_asmbl_35531.p1, terminal, 25027, 25059
-recovered pasa_asmbl_35531.p1, internal, 21452, 21662
-recovered pasa_asmbl_35531.p1, internal, 21889, 21945
-recovered pasa_asmbl_35531.p1, internal, 22524, 22592
-recovered pasa_asmbl_35531.p1, internal, 22942, 23115
-recovered pasa_asmbl_35531.p1, internal, 23364, 23476
-recovered pasa_asmbl_35531.p1, internal, 23558, 23624
-recovered pasa_asmbl_35531.p1, internal, 23732, 23904
-recovered pasa_asmbl_35531.p1, internal, 24037, 24118
-recovered pasa_asmbl_35531.p1, internal, 24238, 24423
-recovered pasa_asmbl_35531.p1, internal, 24518, 24661
Valid prediction for GlimmerHMM_glimmerT_55455-T1
Valid prediction for snap_scaffold_26-snap.856-T1
Valid prediction for snap_scaffold_26-snap.892-T1
Sorry, intron length (8) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.872-T1
Valid prediction for snap_scaffold_26-snap.858-T1
Valid prediction for GlimmerHMM_glimmerT_55464-T1
Valid prediction for snap_scaffold_26-snap.870-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.860-T1
Valid prediction for Augustus_model.g36732.t1
Valid prediction for snap_scaffold_26-snap.857-T1
Valid prediction for GlimmerHMM_glimmerT_55456-T1
Valid prediction for snap_scaffold_26-snap.868-T1
Valid prediction for snap_scaffold_26-snap.885-T1
Valid prediction for GlimmerHMM_glimmerT_55457-T1
Valid prediction for Augustus_model.g36734.t1
Valid prediction for snap_scaffold_26-snap.876-T1
Valid prediction for snap_scaffold_26-snap.866-T1
Valid prediction for snap_scaffold_26-snap.878-T1
Valid prediction for snap_scaffold_26-snap.863-T1
Valid prediction for snap_scaffold_26-snap.873-T1
Valid prediction for snap_scaffold_26-snap.861-T1
Valid prediction for HiQ_model.g36741.t1
Valid prediction for snap_scaffold_26-snap.879-T1
Valid prediction for snap_scaffold_26-snap.864-T1
Valid prediction for snap_scaffold_26-snap.877-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.886-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.862-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20330, rend_intergenic: 5784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27897, rend_intergenic: 22789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44331, rend_intergenic: 27956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48745, rend_intergenic: 44331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50375, rend_intergenic: 48863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58526, rend_intergenic: 50414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58690, rend_intergenic: 58557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70310, rend_intergenic: 64092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77154, rend_intergenic: 75816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87510, rend_intergenic: 78553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91890, rend_intergenic: 88500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115494, rend_intergenic: 110686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121570, rend_intergenic: 117853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139640, rend_intergenic: 132919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 142695
-exon list size: 487


building trellis

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66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 20330, rend_intergenic: 5784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27897, rend_intergenic: 22789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44331, rend_intergenic: 27956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48745, rend_intergenic: 44331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50375, rend_intergenic: 48863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58526, rend_intergenic: 50414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58690, rend_intergenic: 58557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70310, rend_intergenic: 64092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77154, rend_intergenic: 75816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87510, rend_intergenic: 78553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91890, rend_intergenic: 88500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115494, rend_intergenic: 110686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121570, rend_intergenic: 117853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139640, rend_intergenic: 132919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support