-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_5848069-6003720

-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.84900_t
Valid prediction for CodingQuarry_transcript_32506-T1
Valid prediction for GeneMark_model.84894_t
Valid prediction for Augustus_model.g32803.t1
Couldn't classify 148562, 148606
Couldn't classify 150752, 150902
Sorry, prediction pasa_asmbl_28623.p1 fails validation.
(CTG)	 TC	148562-148606	GT	GGG
(ATC)	 AG	149026-149169	GT	AGG
(GAC)	 AG	149274-149442	GT	AGG
(GGG)	 AG	149544-149642	GT	AGG
(GTT)	 AG	149989-150154	GT	AAG
(GGG)	 AG	150752-150902	GT	TGG
-recovered pasa_asmbl_28623.p1, internal, 149026, 149169
-recovered pasa_asmbl_28623.p1, internal, 149274, 149442
-recovered pasa_asmbl_28623.p1, internal, 149544, 149642
-recovered pasa_asmbl_28623.p1, internal, 149989, 150154
-recovered pasa_asmbl_28623.p1, internal, 150752, 150902
Valid prediction for GlimmerHMM_glimmerT_48960-T1
Valid prediction for snap_scaffold_21-snap.1212-T1
Valid prediction for snap_scaffold_21-snap.1184-T1
Valid prediction for GeneMark_model.84923_t
Valid prediction for GeneMark_model.84922_t
Valid prediction for snap_scaffold_21-snap.1191-T1
Valid prediction for snap_scaffold_21-snap.1198-T1
Valid prediction for Augustus_model.g32819.t1
Couldn't classify 147404, 147712
Couldn't classify 148247, 148489
Sorry, prediction pasa_asmbl_28622.p1 fails validation.
(AAG)	 AG	147404-147712	GT	AGG
(ATT)	 AG	147825-147925	GT	AGG
(GTT)	 AG	148004-148139	GT	TGG
(TCC)	 AG	148247-148489	GA	CCG
-recovered pasa_asmbl_28622.p1, internal, 147404, 147712
-recovered pasa_asmbl_28622.p1, internal, 147825, 147925
-recovered pasa_asmbl_28622.p1, internal, 148004, 148139
Valid prediction for GlimmerHMM_glimmerT_48979-T1
Couldn't classify 120515, 120530
Sorry, prediction pasa_asmbl_28616.p1 fails validation.
(ACC)	 GA	120515-120530	GT	AGG
(AGG)	 AG	121669-121876	GT	AGG
(TGA)	 AG	122129-122247	GT	TGG
(ACG)	 AG	122428-122563	GT	AGG
(GTG)	 AG	122763-122886	GT	GGG
(GAC)	 AG	123572-123721	GT	AGG
(CTG)	 AG	123834-123999	GT	AGG
(GCG)	 AG	124120-124324	GT	AGG
(AAC)	 AG	124440-124508	GT	CAG
(GCT)	 AG	124635-124837	GT	AGG
(GGA)	 AG	124938-125035	GT	GGG
(GGG)	 AG	125314-125530	GT	AGG
(CCA)	 AG	125651-125749	GT	TGG
(GGA)	 AG	125836-125989	GT	AGG
(GAC)	 AG	126115-126283	GT	TGG
(GTG)	 AG	126370-126488	GT	AGG
(TGG)	 AG	126955-127111	GT	AGG
(GAT)	 AG	127266-127466	GT	AGG
(GGG)	 AG	127604-127780	GT	TGG
(TTG)	 AG	127874-128021	GT	CGG
(CCC)	 AG	128181-128271	GT	AGG
(GGG)	 AG	128365-128489	GT	AGG
(TTC)	 AG	128653-128799	GT	AGG
(ATA)	 AG	128920-129010	GT	TGG
(CCG)	 AG	129132-129264	TG	AAT
add_exon() Sorry, pasa_asmbl_28616.p1 128653-128799-terminal-1 is invalid.
-recovered pasa_asmbl_28616.p1, terminal, 128653, 128799
-recovered pasa_asmbl_28616.p1, terminal, 129132, 129264
-recovered pasa_asmbl_28616.p1, internal, 121669, 121876
-recovered pasa_asmbl_28616.p1, internal, 122129, 122247
-recovered pasa_asmbl_28616.p1, internal, 122428, 122563
-recovered pasa_asmbl_28616.p1, internal, 122763, 122886
-recovered pasa_asmbl_28616.p1, internal, 123572, 123721
-recovered pasa_asmbl_28616.p1, internal, 123834, 123999
-recovered pasa_asmbl_28616.p1, internal, 124120, 124324
-recovered pasa_asmbl_28616.p1, internal, 124440, 124508
-recovered pasa_asmbl_28616.p1, internal, 124635, 124837
-recovered pasa_asmbl_28616.p1, internal, 124938, 125035
-recovered pasa_asmbl_28616.p1, internal, 125314, 125530
-recovered pasa_asmbl_28616.p1, internal, 125651, 125749
-recovered pasa_asmbl_28616.p1, internal, 125836, 125989
-recovered pasa_asmbl_28616.p1, internal, 126115, 126283
-recovered pasa_asmbl_28616.p1, internal, 126370, 126488
-recovered pasa_asmbl_28616.p1, internal, 126955, 127111
-recovered pasa_asmbl_28616.p1, internal, 127266, 127466
-recovered pasa_asmbl_28616.p1, internal, 127604, 127780
-recovered pasa_asmbl_28616.p1, internal, 127874, 128021
-recovered pasa_asmbl_28616.p1, internal, 128181, 128271
-recovered pasa_asmbl_28616.p1, internal, 128365, 128489
-recovered pasa_asmbl_28616.p1, internal, 128653, 128799
-recovered pasa_asmbl_28616.p1, internal, 128920, 129010
Valid prediction for GeneMark_model.84907_t
Valid prediction for snap_scaffold_21-snap.1214-T1
Valid prediction for GeneMark_model.84916_t
Valid prediction for GeneMark_model.84898_t
Valid prediction for Augustus_model.g32797.t1
Valid prediction for CodingQuarry_transcript_32511-T1
Couldn't classify 145019, 145118
Couldn't classify 145501, 145665
Sorry, prediction pasa_asmbl_28620.p2 fails validation.
(CAG)	 GG	145019-145118	GT	AGG
(CTC)	 AG	145238-145410	GT	GGG
(AGT)	 AG	145501-145665	GG	AGG
-recovered pasa_asmbl_28620.p2, internal, 145238, 145410
Valid prediction for GeneMark_model.84897_t
Valid prediction for HiQ_model.g32798.t1
Valid prediction for GeneMark_model.84918_t
Valid prediction for GlimmerHMM_glimmerT_48970-T1
Valid prediction for GlimmerHMM_glimmerT_48981-T1
Valid prediction for GeneMark_model.84909_t
Valid prediction for snap_scaffold_21-snap.1177-T1
Valid prediction for snap_scaffold_21-snap.1208-T1
Valid prediction for pasa_asmbl_28612.p1
Valid prediction for snap_scaffold_21-snap.1210-T1
Valid prediction for GlimmerHMM_glimmerT_48963-T1
Valid prediction for Augustus_model.g32807.t1
Valid prediction for GlimmerHMM_glimmerT_48969-T1
Valid prediction for GeneMark_model.84911_t
Valid prediction for GlimmerHMM_glimmerT_48958-T1
Valid prediction for GlimmerHMM_glimmerT_48983-T1
Valid prediction for GlimmerHMM_glimmerT_48973-T1
Valid prediction for Augustus_model.g32808.t1
Valid prediction for snap_scaffold_21-snap.1205-T1
Valid prediction for GlimmerHMM_glimmerT_48978-T1
Valid prediction for GlimmerHMM_glimmerT_48975-T1
Valid prediction for snap_scaffold_21-snap.1181-T1
Valid prediction for GeneMark_model.84910_t
Valid prediction for GeneMark_model.84913_t
Valid prediction for Augustus_model.g32809.t1
Valid prediction for snap_scaffold_21-snap.1200-T1
Valid prediction for GlimmerHMM_glimmerT_48968-T1
Valid prediction for snap_scaffold_21-snap.1176-T1
Valid prediction for snap_scaffold_21-snap.1183-T1
Valid prediction for pasa_asmbl_28611.p1
Valid prediction for GeneMark_model.84903_t
Valid prediction for HiQ_model.g32802.t1
Valid prediction for Augustus_model.g32810.t1
Valid prediction for GlimmerHMM_glimmerT_48959-T1
Valid prediction for GlimmerHMM_glimmerT_48984-T1
Valid prediction for GeneMark_model.84905_t
Valid prediction for GlimmerHMM_glimmerT_48982-T1
Valid prediction for snap_scaffold_21-snap.1186-T1
Valid prediction for snap_scaffold_21-snap.1196-T1
Valid prediction for HiQ_model.g32817.t1
Valid prediction for snap_scaffold_21-snap.1190-T1
Valid prediction for pasa_asmbl_28613.p1
Valid prediction for Augustus_model.g32801.t1
Valid prediction for GlimmerHMM_glimmerT_48962-T1
Couldn't classify 146316, 146356
Couldn't classify 147060, 147106
Sorry, prediction pasa_asmbl_28621.p1 fails validation.
(ACC)	 CC	146316-146356	GT	AGG
(TCG)	 AG	146462-146636	GT	AGG
(GTG)	 AG	146750-146882	GT	AGG
(TGA)	 AG	147060-147106	GT	CCG
-recovered pasa_asmbl_28621.p1, internal, 146462, 146636
-recovered pasa_asmbl_28621.p1, internal, 146750, 146882
-recovered pasa_asmbl_28621.p1, internal, 147060, 147106
Valid prediction for Augustus_model.g32816.t1
Valid prediction for snap_scaffold_21-snap.1203-T1
Valid prediction for snap_scaffold_21-snap.1206-T1
Valid prediction for CodingQuarry_transcript_32508-T1
Valid prediction for snap_scaffold_21-snap.1185-T1
Valid prediction for Augustus_model.g32813.t1
Couldn't classify 143312, 143433
Couldn't classify 143929, 144055
Sorry, prediction pasa_asmbl_29032.p1 fails validation.
(AGT)	 TC	143312-143433	GT	AAG
(GGC)	 AG	143613-143774	GT	AGG
(CCA)	 AG	143929-144055	AG	GGA
-recovered pasa_asmbl_29032.p1, internal, 143613, 143774
Valid prediction for GlimmerHMM_glimmerT_48972-T1
Valid prediction for snap_scaffold_21-snap.1182-T1
Valid prediction for GlimmerHMM_glimmerT_48971-T1
Valid prediction for GeneMark_model.84920_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.84908_t
Valid prediction for Augustus_model.g32811.t1
Valid prediction for Augustus_model.g32805.t1
Valid prediction for GeneMark_model.84919_t
Valid prediction for snap_scaffold_21-snap.1192-T1
Valid prediction for snap_scaffold_21-snap.1211-T1
Valid prediction for Augustus_model.g32800.t1
Valid prediction for pasa_asmbl_27738.p1
Couldn't classify 99045, 99101
Couldn't classify 105152, 105250
Sorry, prediction pasa_asmbl_28240.p1 fails validation.
(TAC)	 GC	99045-99101	GT	GGG
(GTG)	 AG	101729-101871	GT	AAG
(CCG)	 AG	101964-102116	GT	AGG
(TCT)	 AG	102272-102461	GT	ACG
(ATT)	 AG	104305-104370	GT	TGG
(TAT)	 AG	105152-105250	GT	TGG
-recovered pasa_asmbl_28240.p1, internal, 101729, 101871
-recovered pasa_asmbl_28240.p1, internal, 101964, 102116
-recovered pasa_asmbl_28240.p1, internal, 102272, 102461
-recovered pasa_asmbl_28240.p1, internal, 104305, 104370
-recovered pasa_asmbl_28240.p1, internal, 105152, 105250
Valid prediction for GlimmerHMM_glimmerT_48964-T1
Valid prediction for snap_scaffold_21-snap.1180-T1
Valid prediction for GeneMark_model.84902_t
Valid prediction for snap_scaffold_21-snap.1209-T1
Valid prediction for CodingQuarry_transcript_32507-T1
Valid prediction for snap_scaffold_21-snap.1199-T1
Valid prediction for snap_scaffold_21-snap.1188-T1
Valid prediction for GeneMark_model.84896_t
Valid prediction for GlimmerHMM_glimmerT_48974-T1
Valid prediction for pasa_asmbl_27730.p1
Valid prediction for HiQ_model.g32818.t1
Valid prediction for GeneMark_model.84901_t
Valid prediction for GeneMark_model.84912_t
Valid prediction for GlimmerHMM_glimmerT_48980-T1
Valid prediction for GeneMark_model.84906_t
Valid prediction for GlimmerHMM_glimmerT_48977-T1
Valid prediction for GlimmerHMM_glimmerT_48976-T1
Valid prediction for GeneMark_model.84904_t
Valid prediction for GlimmerHMM_glimmerT_48967-T1
Valid prediction for GeneMark_model.84895_t
Valid prediction for snap_scaffold_21-snap.1204-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1187-T1
Valid prediction for Augustus_model.g32814.t1
Valid prediction for snap_scaffold_21-snap.1213-T1
Valid prediction for GeneMark_model.84914_t
Valid prediction for snap_scaffold_21-snap.1197-T1
Valid prediction for HiQ_model.g32799.t1
Couldn't classify 143139, 143277
Sorry, prediction pasa_asmbl_27731.p1 fails validation.
(CCC)	 CT	143139-143277	GT	AGG
(TTA)	 AG	143390-143446	GT	GGG
(TCA)	 AG	143559-143624	GT	GTG
(ACT)	 AG	143741-144261	AC	GAA
-recovered pasa_asmbl_27731.p1, terminal, 143741, 144261
-recovered pasa_asmbl_27731.p1, internal, 143390, 143446
-recovered pasa_asmbl_27731.p1, internal, 143559, 143624
Valid prediction for GlimmerHMM_glimmerT_48965-T1
Valid prediction for snap_scaffold_21-snap.1178-T1
Valid prediction for GeneMark_model.84917_t
Valid prediction for pasa_asmbl_27736.p1
Valid prediction for CodingQuarry_transcript_32509-T1
Valid prediction for GeneMark_model.84921_t
Valid prediction for snap_scaffold_21-snap.1194-T1
Valid prediction for Augustus_model.g32806.t1
Valid prediction for snap_scaffold_21-snap.1202-T1
Valid prediction for Augustus_model.g32812.t1
Valid prediction for GeneMark_model.84915_t
Valid prediction for snap_scaffold_21-snap.1201-T1
Valid prediction for Augustus_model.g32804.t1
Valid prediction for snap_scaffold_21-snap.1207-T1
Valid prediction for Augustus_model.g32815.t1
Valid prediction for snap_scaffold_21-snap.1195-T1
Valid prediction for snap_scaffold_21-snap.1193-T1
Valid prediction for GlimmerHMM_glimmerT_48961-T1
Valid prediction for GeneMark_model.84924_t
Valid prediction for snap_scaffold_21-snap.1179-T1
Valid prediction for GlimmerHMM_glimmerT_48966-T1
Valid prediction for snap_scaffold_21-snap.1189-T1
Valid prediction for GeneMark_model.84899_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51018, rend_intergenic: 46493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55010, rend_intergenic: 53624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61125, rend_intergenic: 59215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79586, rend_intergenic: 75704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84003, rend_intergenic: 82754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86140, rend_intergenic: 84351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94217, rend_intergenic: 88885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109730, rend_intergenic: 106094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139869, rend_intergenic: 134273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144130, rend_intergenic: 143902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147534, rend_intergenic: 144201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152840, rend_intergenic: 150403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 155652
-exon list size: 599


building trellis

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65.1    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.7    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 51018, rend_intergenic: 46493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55010, rend_intergenic: 53624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61125, rend_intergenic: 59215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79586, rend_intergenic: 75704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84003, rend_intergenic: 82754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86140, rend_intergenic: 84351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94217, rend_intergenic: 88885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109730, rend_intergenic: 106094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139869, rend_intergenic: 134273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144130, rend_intergenic: 143902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147534, rend_intergenic: 144201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152840, rend_intergenic: 150403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support