-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_15556139-15733332

-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_5-snap.2858-T1
Couldn't classify 126930, 127094
Sorry, prediction pasa_asmbl_46008.p1 fails validation.
(TGC)	 CG	126930-127094	GT	AGG
(CTG)	 AG	127235-127307	GT	AGG
(AGT)	 AG	127836-127924	TC	AAT
-recovered pasa_asmbl_46008.p1, terminal, 127836, 127924
-recovered pasa_asmbl_46008.p1, internal, 127235, 127307
Valid prediction for Augustus_model.g8800.t1
Valid prediction for GlimmerHMM_glimmerT_13254-T1
Valid prediction for CodingQuarry_transcript_52399-T1
Valid prediction for GlimmerHMM_glimmerT_13257-T1
Valid prediction for Augustus_model.g8809.t1
Valid prediction for GlimmerHMM_glimmerT_13233-T1
Valid prediction for snap_scaffold_5-snap.2852-T1
Valid prediction for snap_scaffold_5-snap.2876-T1
Valid prediction for snap_scaffold_5-snap.2848-T1
Valid prediction for CodingQuarry_transcript_52400-T1
Valid prediction for snap_scaffold_5-snap.2861-T1
Valid prediction for GlimmerHMM_glimmerT_13227-T1
Valid prediction for GlimmerHMM_glimmerT_13241-T1
Valid prediction for snap_scaffold_5-snap.2844-T1
Couldn't classify 147327, 147482
Sorry, prediction pasa_asmbl_46012.p1 fails validation.
(TTG)	 GC	147327-147482	GT	TGG
(ACA)	 AG	149947-150073	GT	TGG
(ACA)	 AG	150229-150404	GT	AGG
(GAG)	 AG	151349-151498	GG	GAG
-recovered pasa_asmbl_46012.p1, terminal, 151349, 151498
-recovered pasa_asmbl_46012.p1, internal, 149947, 150073
-recovered pasa_asmbl_46012.p1, internal, 150229, 150404
Valid prediction for snap_scaffold_5-snap.2849-T1
Valid prediction for snap_scaffold_5-snap.2841-T1
Valid prediction for snap_scaffold_5-snap.2862-T1
Valid prediction for GlimmerHMM_glimmerT_13231-T1
Valid prediction for GlimmerHMM_glimmerT_13250-T1
Valid prediction for snap_scaffold_5-snap.2857-T1
Valid prediction for snap_scaffold_5-snap.2859-T1
Valid prediction for Augustus_model.g8805.t1
Valid prediction for snap_scaffold_5-snap.2864-T1
Valid prediction for snap_scaffold_5-snap.2843-T1
Valid prediction for pasa_asmbl_46007.p1
Valid prediction for snap_scaffold_5-snap.2850-T1
Valid prediction for snap_scaffold_5-snap.2882-T1
Valid prediction for snap_scaffold_5-snap.2880-T1
Valid prediction for HiQ_model.g8808.t1
Valid prediction for GlimmerHMM_glimmerT_13224-T1
Valid prediction for snap_scaffold_5-snap.2883-T1
Valid prediction for GlimmerHMM_glimmerT_13240-T1
Valid prediction for GlimmerHMM_glimmerT_13248-T1
Valid prediction for snap_scaffold_5-snap.2874-T1
Couldn't classify 80016, 80369
Sorry, prediction pasa_asmbl_46001.p1 fails validation.
(ATG)	 GT	79293-79554	GT	AGG
(ATG)	 AG	79729-79928	GT	TGG
(TTG)	 AG	80016-80369	AT	GCA
-recovered pasa_asmbl_46001.p1, initial, 79293, 79554
add_exon() Sorry, pasa_asmbl_46001.p1 79729-79928-initial-1 is invalid.
-recovered pasa_asmbl_46001.p1, initial, 79729, 79928
-recovered pasa_asmbl_46001.p1, internal, 79729, 79928
Couldn't classify 119829, 119968
Couldn't classify 120145, 120242
Sorry, prediction CodingQuarry_transcript_52398-T1 fails validation.
(ATG)	 TA	118211-118240	GT	AGG
(CCG)	 AG	118684-118890	GT	AGG
(GGC)	 AG	119481-119587	GT	AGG
(GTT)	 AG	119829-119968	AT	TGA
(ATA)	 AC	120145-120242	GT	TGG
(TTG)	 AG	121151-121244	GT	AGG
(CCA)	 AG	122177-122268	GT	AGG
(GCG)	 AG	122362-122434	GT	CAG
(GCA)	 AG	122509-122567	GT	CTG
(GTG)	 AG	122850-122998	GT	AGG
(GGA)	 AG	124009-124190	GT	AGG
(AGC)	 AG	124796-124893	GT	AGG
(GTT)	 AG	125148-125228	GT	ACG
(GAC)	 AG	126957-127094	GT	AGG
(CTG)	 AG	127235-127307	GT	AGG
(AGT)	 AG	127836-127924	TC	AAT
-recovered CodingQuarry_transcript_52398-T1, initial, 118211, 118240
-recovered CodingQuarry_transcript_52398-T1, terminal, 121151, 121244
-recovered CodingQuarry_transcript_52398-T1, terminal, 127836, 127924
-recovered CodingQuarry_transcript_52398-T1, internal, 118684, 118890
-recovered CodingQuarry_transcript_52398-T1, internal, 119481, 119587
-recovered CodingQuarry_transcript_52398-T1, internal, 121151, 121244
-recovered CodingQuarry_transcript_52398-T1, internal, 122177, 122268
-recovered CodingQuarry_transcript_52398-T1, internal, 122362, 122434
-recovered CodingQuarry_transcript_52398-T1, internal, 122509, 122567
-recovered CodingQuarry_transcript_52398-T1, internal, 122850, 122998
-recovered CodingQuarry_transcript_52398-T1, internal, 124009, 124190
-recovered CodingQuarry_transcript_52398-T1, internal, 124796, 124893
-recovered CodingQuarry_transcript_52398-T1, internal, 125148, 125228
-recovered CodingQuarry_transcript_52398-T1, internal, 126957, 127094
-recovered CodingQuarry_transcript_52398-T1, internal, 127235, 127307
Valid prediction for snap_scaffold_5-snap.2867-T1
Valid prediction for snap_scaffold_5-snap.2871-T1
Valid prediction for pasa_asmbl_46010.p1
Valid prediction for GlimmerHMM_glimmerT_13253-T1
Valid prediction for Augustus_model.g8811.t1
Valid prediction for GlimmerHMM_glimmerT_13230-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_5-snap.2860-T1
Valid prediction for snap_scaffold_5-snap.2845-T1
Couldn't classify 19184, 19223
Sorry, prediction pasa_asmbl_44718.p1 fails validation.
(CTA)	 CT	19184-19223	GT	AGG
(CCG)	 AG	19916-20089	GT	CGG
(GAC)	 AG	20192-20419	GT	CCG
(GAG)	 AG	20624-20742	GT	AGG
(TTT)	 AG	21094-21222	GT	TGG
(GTC)	 AG	21466-21637	GT	AGG
(TCT)	 AG	21959-22088	GT	TGG
(GAA)	 AG	22261-22364	GT	GGG
(GTG)	 AG	22459-22701	GT	AGG
(GCT)	 AG	22902-23177	GT	GGG
(AGA)	 AG	23337-23497	GT	ATG
(ATC)	 AG	23718-23854	GT	GTG
(GAT)	 AG	24047-24194	CA	GAC
-recovered pasa_asmbl_44718.p1, terminal, 24047, 24194
-recovered pasa_asmbl_44718.p1, internal, 19916, 20089
-recovered pasa_asmbl_44718.p1, internal, 20192, 20419
-recovered pasa_asmbl_44718.p1, internal, 20624, 20742
-recovered pasa_asmbl_44718.p1, internal, 21094, 21222
-recovered pasa_asmbl_44718.p1, internal, 21466, 21637
-recovered pasa_asmbl_44718.p1, internal, 21959, 22088
-recovered pasa_asmbl_44718.p1, internal, 22261, 22364
-recovered pasa_asmbl_44718.p1, internal, 22459, 22701
-recovered pasa_asmbl_44718.p1, internal, 22902, 23177
-recovered pasa_asmbl_44718.p1, internal, 23337, 23497
-recovered pasa_asmbl_44718.p1, internal, 23718, 23854
Valid prediction for GlimmerHMM_glimmerT_13256-T1
Valid prediction for pasa_asmbl_44707.p1
Valid prediction for GlimmerHMM_glimmerT_13251-T1
Valid prediction for snap_scaffold_5-snap.2881-T1
Valid prediction for snap_scaffold_5-snap.2868-T1
Valid prediction for GlimmerHMM_glimmerT_13225-T1
Valid prediction for GlimmerHMM_glimmerT_13261-T1
Valid prediction for GlimmerHMM_glimmerT_13242-T1
Valid prediction for pasa_asmbl_44705.p1
Valid prediction for GlimmerHMM_glimmerT_13243-T1
Valid prediction for snap_scaffold_5-snap.2846-T1
Valid prediction for Augustus_model.g8813.t1
Valid prediction for snap_scaffold_5-snap.2855-T1
Valid prediction for snap_scaffold_5-snap.2853-T1
Valid prediction for GlimmerHMM_glimmerT_13252-T1
Valid prediction for snap_scaffold_5-snap.2875-T1
Couldn't classify 86123, 86305
Couldn't classify 86763, 86807
Sorry, prediction pasa_asmbl_45006.p1 fails validation.
(CTG)	 AT	86123-86305	GC	AGG
(GTG)	 AG	86426-86551	GT	GGG
(GTG)	 AG	86763-86807	AA	AGA
-recovered pasa_asmbl_45006.p1, internal, 86426, 86551
Valid prediction for HiQ_model.g8803.t1
Valid prediction for HiQ_model.g8812.t1
Valid prediction for GlimmerHMM_glimmerT_13226-T1
Valid prediction for snap_scaffold_5-snap.2863-T1
Valid prediction for CodingQuarry_transcript_52396-T1
Valid prediction for Augustus_model.g8814.t1
Valid prediction for snap_scaffold_5-snap.2866-T1
Valid prediction for snap_scaffold_5-snap.2877-T1
Valid prediction for pasa_asmbl_44711.p1
Valid prediction for snap_scaffold_5-snap.2869-T1
Valid prediction for GlimmerHMM_glimmerT_13244-T1
Valid prediction for snap_scaffold_5-snap.2842-T1
Valid prediction for snap_scaffold_5-snap.2865-T1
Valid prediction for GlimmerHMM_glimmerT_13232-T1
Valid prediction for GlimmerHMM_glimmerT_13237-T1
Valid prediction for HiQ_model.g8802.t1
Valid prediction for Augustus_model.g8801.t1
Valid prediction for GlimmerHMM_glimmerT_13246-T1
Valid prediction for CodingQuarry_transcript_52394-T1
Valid prediction for GlimmerHMM_glimmerT_13259-T1
Valid prediction for GlimmerHMM_glimmerT_13228-T1
Couldn't classify 36982, 37018
Sorry, prediction pasa_asmbl_44717.p1 fails validation.
(CAA)	 TG	36982-37018	GT	GGG
(GTG)	 AG	37636-37723	GT	AGG
(TGT)	 AG	37984-38203	CG	AAC
-recovered pasa_asmbl_44717.p1, terminal, 37984, 38203
-recovered pasa_asmbl_44717.p1, internal, 37636, 37723
Valid prediction for CodingQuarry_transcript_52395-T1
Valid prediction for snap_scaffold_5-snap.2856-T1
Valid prediction for snap_scaffold_5-snap.2851-T1
Valid prediction for Augustus_model.g8804.t1
Valid prediction for CodingQuarry_transcript_52397-T1
Valid prediction for GlimmerHMM_glimmerT_13236-T1
Valid prediction for GlimmerHMM_glimmerT_13234-T1
Valid prediction for snap_scaffold_5-snap.2870-T1
Valid prediction for GlimmerHMM_glimmerT_13249-T1
Valid prediction for snap_scaffold_5-snap.2854-T1
Valid prediction for Augustus_model.g8810.t1
Valid prediction for Augustus_model.g8806.t1
Valid prediction for GlimmerHMM_glimmerT_13260-T1
Valid prediction for GlimmerHMM_glimmerT_13239-T1
Valid prediction for GlimmerHMM_glimmerT_13229-T1
Valid prediction for snap_scaffold_5-snap.2879-T1
Valid prediction for GlimmerHMM_glimmerT_13235-T1
Couldn't classify 93238, 93396
Couldn't classify 94022, 94132
Sorry, prediction pasa_asmbl_44991.p1 fails validation.
(CTG)	 GT	93238-93396	GT	AGG
(AGT)	 AG	93590-93751	GT	AGG
(ATG)	 AG	94022-94132	CC	AAC
-recovered pasa_asmbl_44991.p1, internal, 93590, 93751
Valid prediction for snap_scaffold_5-snap.2872-T1
Valid prediction for GlimmerHMM_glimmerT_13238-T1
Valid prediction for Augustus_model.g8807.t1
Valid prediction for GlimmerHMM_glimmerT_13247-T1
Valid prediction for CodingQuarry_transcript_52393-T1
Valid prediction for snap_scaffold_5-snap.2878-T1
Valid prediction for GlimmerHMM_glimmerT_13255-T1
Valid prediction for GlimmerHMM_glimmerT_13245-T1
Valid prediction for pasa_asmbl_44703.p3
Valid prediction for snap_scaffold_5-snap.2873-T1
Valid prediction for GlimmerHMM_glimmerT_13258-T1
Valid prediction for snap_scaffold_5-snap.2847-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 64163, rend_intergenic: 64160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6983, rend_intergenic: 4658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18503, rend_intergenic: 7110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31921, rend_intergenic: 18560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55339, rend_intergenic: 32486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56539, rend_intergenic: 55403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103763, rend_intergenic: 86271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110232, rend_intergenic: 110173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116746, rend_intergenic: 111401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120006, rend_intergenic: 118665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123269, rend_intergenic: 120131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125669, rend_intergenic: 124019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127924, rend_intergenic: 125760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134013, rend_intergenic: 133255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142212, rend_intergenic: 138992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151498, rend_intergenic: 147294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157283, rend_intergenic: 153001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166544, rend_intergenic: 163300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169114, rend_intergenic: 166812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175558, rend_intergenic: 169156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177194
-exon list size: 543


building trellis

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77.4    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 64163, rend_intergenic: 64160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6983, rend_intergenic: 4658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18503, rend_intergenic: 7110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31921, rend_intergenic: 18560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55339, rend_intergenic: 32486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56539, rend_intergenic: 55403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103763, rend_intergenic: 86271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110232, rend_intergenic: 110173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116746, rend_intergenic: 111401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120006, rend_intergenic: 118665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123269, rend_intergenic: 120131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125669, rend_intergenic: 124019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127924, rend_intergenic: 125760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134013, rend_intergenic: 133255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142212, rend_intergenic: 138992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151498, rend_intergenic: 147294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157283, rend_intergenic: 153001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166544, rend_intergenic: 163300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169114, rend_intergenic: 166812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175558, rend_intergenic: 169156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support