-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_11574822-11795454

-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.65113_t
Valid prediction for snap_scaffold_15-snap.2386-T1
Valid prediction for snap_scaffold_15-snap.2422-T1
Valid prediction for Augustus_model.g25344.t1
Valid prediction for GlimmerHMM_glimmerT_37835-T1
Valid prediction for Augustus_model.g25360.t1
Valid prediction for snap_scaffold_15-snap.2404-T1
Valid prediction for GlimmerHMM_glimmerT_37842-T1
Valid prediction for GeneMark_model.65117_t
Valid prediction for snap_scaffold_15-snap.2415-T1
Valid prediction for HiQ_model.g25357.t1
Valid prediction for GlimmerHMM_glimmerT_37834-T1
Valid prediction for GeneMark_model.65104_t
Valid prediction for GeneMark_model.65138_t
Valid prediction for GlimmerHMM_glimmerT_37828-T1
Valid prediction for GeneMark_model.65094_t
Valid prediction for snap_scaffold_15-snap.2421-T1
Valid prediction for GeneMark_model.65106_t
Valid prediction for snap_scaffold_15-snap.2412-T1
Valid prediction for Augustus_model.g25363.t1
Valid prediction for snap_scaffold_15-snap.2411-T1
Valid prediction for Augustus_model.g25359.t1
Valid prediction for CodingQuarry_transcript_18110-T1
Valid prediction for GlimmerHMM_glimmerT_37808-T1
Valid prediction for snap_scaffold_15-snap.2385-T1
Valid prediction for GlimmerHMM_glimmerT_37816-T1
Valid prediction for snap_scaffold_15-snap.2408-T1
Valid prediction for GlimmerHMM_glimmerT_37815-T1
Valid prediction for GeneMark_model.65115_t
Couldn't classify 148633, 148959
Sorry, prediction pasa_asmbl_14451.p3 fails validation.
(AAC)	 TC	148633-148959	CC	CTC
Valid prediction for snap_scaffold_15-snap.2397-T1
Valid prediction for GeneMark_model.65137_t
Valid prediction for GlimmerHMM_glimmerT_37819-T1
Valid prediction for snap_scaffold_15-snap.2396-T1
Valid prediction for snap_scaffold_15-snap.2403-T1
Valid prediction for snap_scaffold_15-snap.2384-T1
Valid prediction for snap_scaffold_15-snap.2394-T1
Valid prediction for GeneMark_model.65096_t
Valid prediction for GlimmerHMM_glimmerT_37809-T1
Valid prediction for GlimmerHMM_glimmerT_37836-T1
Valid prediction for GeneMark_model.65120_t
Valid prediction for snap_scaffold_15-snap.2419-T1
Valid prediction for GlimmerHMM_glimmerT_37822-T1
Valid prediction for GeneMark_model.65098_t
Valid prediction for snap_scaffold_15-snap.2398-T1
Valid prediction for GeneMark_model.65142_t
Valid prediction for Augustus_model.g25349.t1
Valid prediction for GeneMark_model.65102_t
Valid prediction for HiQ_model.g25361.t1
Valid prediction for GlimmerHMM_glimmerT_37810-T1
Valid prediction for GeneMark_model.65132_t
Valid prediction for GeneMark_model.65128_t
Valid prediction for snap_scaffold_15-snap.2413-T1
Valid prediction for GeneMark_model.65100_t
Valid prediction for GlimmerHMM_glimmerT_37840-T1
Valid prediction for snap_scaffold_15-snap.2389-T1
Valid prediction for GeneMark_model.65141_t
Couldn't classify 149134, 149307
Couldn't classify 152713, 152744
Sorry, prediction pasa_asmbl_14891.p1 fails validation.
(ATA)	 TG	149134-149307	GT	GGG
(GAT)	 AG	149412-149568	GT	AGG
(GTG)	 AG	149771-149859	GT	AAG
(CTG)	 AG	149951-150004	GT	AGG
(GGA)	 AG	150119-150221	GT	ACG
(AAA)	 AG	150364-150432	GT	AGG
(TGA)	 AG	150521-150587	GT	CGG
(GTT)	 AG	150761-150867	GT	GGG
(ATT)	 AG	150993-151053	GT	GGG
(CAA)	 AG	151224-151426	GC	AGG
(ATC)	 AG	151563-151607	GT	TGG
(ACT)	 AG	151702-151800	GT	AGG
(GGT)	 AG	152055-152119	GT	AGG
(TTC)	 AG	152241-152322	GT	TGG
(GGG)	 AG	152713-152744	GA	GGG
-recovered pasa_asmbl_14891.p1, terminal, 151702, 151800
-recovered pasa_asmbl_14891.p1, internal, 149412, 149568
-recovered pasa_asmbl_14891.p1, internal, 149771, 149859
-recovered pasa_asmbl_14891.p1, internal, 149951, 150004
-recovered pasa_asmbl_14891.p1, internal, 150119, 150221
-recovered pasa_asmbl_14891.p1, internal, 150364, 150432
-recovered pasa_asmbl_14891.p1, internal, 150521, 150587
-recovered pasa_asmbl_14891.p1, internal, 150761, 150867
-recovered pasa_asmbl_14891.p1, internal, 150993, 151053
-recovered pasa_asmbl_14891.p1, internal, 151224, 151426
-recovered pasa_asmbl_14891.p1, internal, 151563, 151607
-recovered pasa_asmbl_14891.p1, internal, 151702, 151800
-recovered pasa_asmbl_14891.p1, internal, 152055, 152119
-recovered pasa_asmbl_14891.p1, internal, 152241, 152322
Valid prediction for GlimmerHMM_glimmerT_37844-T1
Valid prediction for snap_scaffold_15-snap.2406-T1
Valid prediction for GlimmerHMM_glimmerT_37830-T1
Valid prediction for Augustus_model.g25352.t1
Valid prediction for GeneMark_model.65109_t
Valid prediction for GlimmerHMM_glimmerT_37837-T1
Valid prediction for GlimmerHMM_glimmerT_37813-T1
Couldn't classify 146950, 147141
Couldn't classify 147436, 147846
Sorry, prediction pasa_asmbl_14450.p1 fails validation.
(TCT)	 CG	146950-147141	GT	AAG
(GCT)	 AG	147436-147846	TT	GGT
Valid prediction for GeneMark_model.65126_t
Valid prediction for GlimmerHMM_glimmerT_37831-T1
Valid prediction for GlimmerHMM_glimmerT_37833-T1
Valid prediction for GlimmerHMM_glimmerT_37824-T1
Valid prediction for GeneMark_model.65111_t
Valid prediction for Augustus_model.g25367.t1
Valid prediction for snap_scaffold_15-snap.2381-T1
Valid prediction for Augustus_model.g25366.t1
Valid prediction for GlimmerHMM_glimmerT_37841-T1
Valid prediction for Augustus_model.g25369.t1
Valid prediction for GeneMark_model.65130_t
Valid prediction for Augustus_model.g25358.t1
Valid prediction for GlimmerHMM_glimmerT_37826-T1
Valid prediction for snap_scaffold_15-snap.2401-T1
Valid prediction for snap_scaffold_15-snap.2418-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_37812-T1
Valid prediction for GeneMark_model.65118_t
Valid prediction for GeneMark_model.65123_t
Valid prediction for Augustus_model.g25365.t1
Valid prediction for snap_scaffold_15-snap.2391-T1
Valid prediction for Augustus_model.g25356.t1
Valid prediction for GeneMark_model.65135_t
Couldn't classify 122575, 122672
Couldn't classify 123745, 123874
Sorry, prediction CodingQuarry_transcript_18109-T1 fails validation.
(ATG)	 AA	117988-118111	GT	TGG
(AGC)	 AG	119268-119367	GT	AAG
(GAA)	 AG	120939-121053	GT	AGG
(GGG)	 AG	121175-121287	GT	GCG
(CCT)	 AG	121643-121704	GT	AGG
(CGA)	 AG	121886-121944	GT	TGG
(GTT)	 AG	122190-122240	GT	TGG
(GGC)	 AG	122346-122454	GT	ACG
(GGT)	 AG	122575-122672	AG	TGA
(ATT)	 GC	123745-123874	GT	GGG
(ACC)	 AG	123979-124071	GT	AGG
(GTT)	 AG	124169-124314	GT	AGG
(TAC)	 AG	124687-124834	GT	GGG
(TCC)	 AG	125119-125201	GT	CGG
(GAC)	 AG	125395-125463	GT	CGG
(CAA)	 AG	125582-125740	GT	ATG
(GAG)	 AG	125944-126105	GT	AGG
(GAG)	 AG	126264-126464	GT	AGG
(GTG)	 AG	127345-127449	GT	AGG
(CTG)	 AG	127623-127760	AC	AGA
-recovered CodingQuarry_transcript_18109-T1, initial, 117988, 118111
-recovered CodingQuarry_transcript_18109-T1, terminal, 127623, 127760
-recovered CodingQuarry_transcript_18109-T1, internal, 119268, 119367
-recovered CodingQuarry_transcript_18109-T1, internal, 120939, 121053
-recovered CodingQuarry_transcript_18109-T1, internal, 121175, 121287
-recovered CodingQuarry_transcript_18109-T1, internal, 121643, 121704
-recovered CodingQuarry_transcript_18109-T1, internal, 121886, 121944
-recovered CodingQuarry_transcript_18109-T1, internal, 122190, 122240
-recovered CodingQuarry_transcript_18109-T1, internal, 122346, 122454
-recovered CodingQuarry_transcript_18109-T1, internal, 123979, 124071
-recovered CodingQuarry_transcript_18109-T1, internal, 124169, 124314
-recovered CodingQuarry_transcript_18109-T1, internal, 124687, 124834
-recovered CodingQuarry_transcript_18109-T1, internal, 125119, 125201
-recovered CodingQuarry_transcript_18109-T1, internal, 125395, 125463
-recovered CodingQuarry_transcript_18109-T1, internal, 125582, 125740
-recovered CodingQuarry_transcript_18109-T1, internal, 125944, 126105
-recovered CodingQuarry_transcript_18109-T1, internal, 126264, 126464
-recovered CodingQuarry_transcript_18109-T1, internal, 127345, 127449
Valid prediction for snap_scaffold_15-snap.2405-T1
Valid prediction for GeneMark_model.65140_t
Valid prediction for GeneMark_model.65134_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 snap_scaffold_15-snap.2383-T1
Valid prediction for snap_scaffold_15-snap.2393-T1
Valid prediction for GlimmerHMM_glimmerT_37814-T1
Valid prediction for snap_scaffold_15-snap.2420-T1
Valid prediction for GeneMark_model.65136_t
Valid prediction for GlimmerHMM_glimmerT_37823-T1
Valid prediction for GeneMark_model.65124_t
Valid prediction for Augustus_model.g25346.t1
Valid prediction for snap_scaffold_15-snap.2399-T1
Valid prediction for snap_scaffold_15-snap.2414-T1
Valid prediction for GeneMark_model.65105_t
Valid prediction for Augustus_model.g25348.t1
Valid prediction for GeneMark_model.65143_t
Valid prediction for GlimmerHMM_glimmerT_37825-T1
Valid prediction for GlimmerHMM_glimmerT_37811-T1
Valid prediction for GlimmerHMM_glimmerT_37817-T1
Valid prediction for snap_scaffold_15-snap.2382-T1
Valid prediction for snap_scaffold_15-snap.2410-T1
Valid prediction for GeneMark_model.65122_t
Valid prediction for Augustus_model.g25353.t1
Valid prediction for CodingQuarry_transcript_18108-T1
Valid prediction for snap_scaffold_15-snap.2390-T1
Valid prediction for Augustus_model.g25345.t1
Valid prediction for GeneMark_model.65129_t
Valid prediction for GeneMark_model.65112_t
Valid prediction for Augustus_model.g25347.t1
Valid prediction for Augustus_model.g25354.t1
Valid prediction for GeneMark_model.65107_t
Valid prediction for snap_scaffold_15-snap.2395-T1
Valid prediction for GlimmerHMM_glimmerT_37821-T1
Valid prediction for GeneMark_model.65139_t
Valid prediction for GeneMark_model.65099_t
Valid prediction for GeneMark_model.65114_t
Valid prediction for GlimmerHMM_glimmerT_37838-T1
Valid prediction for GeneMark_model.65101_t
Valid prediction for GeneMark_model.65108_t
Valid prediction for GeneMark_model.65133_t
Valid prediction for GeneMark_model.65095_t
Valid prediction for GlimmerHMM_glimmerT_37820-T1
Valid prediction for GeneMark_model.65116_t
Valid prediction for GlimmerHMM_glimmerT_37829-T1
Valid prediction for GlimmerHMM_glimmerT_37818-T1
Valid prediction for snap_scaffold_15-snap.2388-T1
Valid prediction for snap_scaffold_15-snap.2387-T1
Valid prediction for Augustus_model.g25362.t1
Valid prediction for GeneMark_model.65131_t
Valid prediction for snap_scaffold_15-snap.2400-T1
Valid prediction for Augustus_model.g25350.t1
Valid prediction for snap_scaffold_15-snap.2417-T1
Valid prediction for GlimmerHMM_glimmerT_37839-T1
Valid prediction for Augustus_model.g25368.t1
Valid prediction for GlimmerHMM_glimmerT_37827-T1
Valid prediction for GeneMark_model.65119_t
Valid prediction for snap_scaffold_15-snap.2416-T1
Valid prediction for GeneMark_model.65097_t
Valid prediction for GlimmerHMM_glimmerT_37843-T1
Valid prediction for Augustus_model.g25351.t1
Valid prediction for snap_scaffold_15-snap.2402-T1
Valid prediction for GeneMark_model.65127_t
Valid prediction for CodingQuarry_transcript_18112-T1
Valid prediction for snap_scaffold_15-snap.2392-T1
Valid prediction for GeneMark_model.65125_t
Valid prediction for Augustus_model.g25364.t1
Valid prediction for snap_scaffold_15-snap.2407-T1
Valid prediction for GlimmerHMM_glimmerT_37832-T1
Valid prediction for snap_scaffold_15-snap.2409-T1
Valid prediction for GeneMark_model.65103_t
Valid prediction for GeneMark_model.65121_t
Valid prediction for Augustus_model.g25355.t1
Valid prediction for GeneMark_model.65144_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14199, rend_intergenic: 7009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32029, rend_intergenic: 18938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45565, rend_intergenic: 32792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51660, rend_intergenic: 47934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57889, rend_intergenic: 51788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87409, rend_intergenic: 70333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89549, rend_intergenic: 87767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98062, rend_intergenic: 94613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114104, rend_intergenic: 102132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127760, rend_intergenic: 119604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135203, rend_intergenic: 132771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140216, rend_intergenic: 137022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 29933, rend_intergenic: 29930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220633
-exon list size: 729


building trellis

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61.7    
61.8    
62.0    
62.1    
62.2    
62.4    
62.5    
62.7    
62.8    
62.9    
63.1    
63.2    
63.3    
63.5    
63.6    
63.7    
63.9    
64.0    
64.2    
64.3    
64.4    
64.6    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.5    
65.7    
65.8    
65.9    
66.1    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.0    
67.2    
67.3    
67.4    
67.6    
67.7    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.1    
69.2    
69.4    
69.5    
69.6    
69.8    
69.9    
70.0    
70.2    
70.3    
70.5    
70.6    
70.7    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.2    
72.4    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.9    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 14199, rend_intergenic: 7009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32029, rend_intergenic: 18938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45565, rend_intergenic: 32792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51660, rend_intergenic: 47934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57889, rend_intergenic: 51788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87409, rend_intergenic: 70333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89549, rend_intergenic: 87767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98062, rend_intergenic: 94613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114104, rend_intergenic: 102132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127760, rend_intergenic: 119604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135203, rend_intergenic: 132771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140216, rend_intergenic: 137022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 29933, rend_intergenic: 29930  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