-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_67

-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_67-snap.7-T1
Valid prediction for GeneMark_model.106360_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.106361_t
Valid prediction for CodingQuarry_transcript_55352-T1
Valid prediction for snap_scaffold_67-snap.2-T1
Couldn't classify 906, 1412
Sorry, prediction pasa_asmbl_49451.p1 fails validation.
(GTA)	 AT	906-1412	AA	CCA
Couldn't classify 24911, 24973
Sorry, prediction snap_scaffold_67-snap.1-T1 fails validation.
(ATG)	 AT	23049-23113	GT	ATG
(GGA)	 AG	23170-23232	GT	GGG
(GGA)	 AG	24242-24308	GT	GGG
(GGC)	 AG	24911-24973	GT	AGG
-recovered snap_scaffold_67-snap.1-T1, initial, 23049, 23113
-recovered snap_scaffold_67-snap.1-T1, internal, 23170, 23232
-recovered snap_scaffold_67-snap.1-T1, internal, 24242, 24308
-recovered snap_scaffold_67-snap.1-T1, internal, 24911, 24973
Valid prediction for snap_scaffold_67-snap.6-T1
Couldn't classify 116, 739
Sorry, prediction Augustus_model.g40686.t1 fails validation.
(TGG)	 AG	116-739	GT	AGG
(TCA)	 AG	856-1443	GT	AGG
(TCC)	 AG	1577-2188	GT	AGG
(ACG)	 AG	2823-3112	GT	AGG
(AGA)	 AG	4970-5234	GT	TGG
(ATT)	 AG	6436-6703	GT	CGG
(GTT)	 AG	7265-7440	GT	AGG
(TTG)	 AG	8750-9043	GT	CGG
(TTG)	 AG	9656-10015	GT	TGG
(TGA)	 AG	10530-10621	GT	AGG
(AGC)	 AG	10825-10891	GT	AGG
(TTG)	 AG	12507-13085	GT	GGG
(GGG)	 AG	13355-13936	GT	AGG
(CCG)	 AG	16259-16870	GT	TGG
(TGA)	 AG	17096-17719	GT	CCG
(GAA)	 AG	17932-18531	GT	CAG
(ATC)	 AG	18698-19306	GT	AAG
(GCT)	 AG	19452-19786	GT	AGG
(GTT)	 AG	19894-19972	GT	AGG
(GTG)	 AG	20180-20325	GT	TGG
(GAC)	 AG	20421-20513	GT	AGG
(GGC)	 AG	20648-20701	GT	CTG
(GGA)	 AG	20810-20881	GT	AGG
(GGT)	 AG	21003-21029	GT	AGG
(GGA)	 AG	21120-21164	GT	AGG
(GGC)	 AG	21431-21484	GT	GGG
(GGT)	 AG	21581-21643	GT	CCG
(GGT)	 AG	21802-22022	GT	GGG
(GGT)	 AG	22325-22360	GT	CTG
(GGA)	 AG	23170-23232	GT	GGG
(GGA)	 AG	24242-24304	GT	GGG
(GGC)	 AG	24911-24938	GA	AGG
add_exon() Sorry, Augustus_model.g40686.t1 1577-2188-terminal-1 is invalid.
-recovered Augustus_model.g40686.t1, terminal, 1577, 2188
add_exon() Sorry, Augustus_model.g40686.t1 13355-13936-terminal-1 is invalid.
-recovered Augustus_model.g40686.t1, terminal, 13355, 13936
-recovered Augustus_model.g40686.t1, terminal, 24911, 24938
-recovered Augustus_model.g40686.t1, internal, 116, 739
-recovered Augustus_model.g40686.t1, internal, 856, 1443
-recovered Augustus_model.g40686.t1, internal, 1577, 2188
-recovered Augustus_model.g40686.t1, internal, 2823, 3112
-recovered Augustus_model.g40686.t1, internal, 4970, 5234
-recovered Augustus_model.g40686.t1, internal, 6436, 6703
-recovered Augustus_model.g40686.t1, internal, 7265, 7440
-recovered Augustus_model.g40686.t1, internal, 8750, 9043
-recovered Augustus_model.g40686.t1, internal, 9656, 10015
-recovered Augustus_model.g40686.t1, internal, 10530, 10621
-recovered Augustus_model.g40686.t1, internal, 10825, 10891
-recovered Augustus_model.g40686.t1, internal, 12507, 13085
-recovered Augustus_model.g40686.t1, internal, 13355, 13936
-recovered Augustus_model.g40686.t1, internal, 16259, 16870
-recovered Augustus_model.g40686.t1, internal, 17096, 17719
-recovered Augustus_model.g40686.t1, internal, 17932, 18531
-recovered Augustus_model.g40686.t1, internal, 18698, 19306
-recovered Augustus_model.g40686.t1, internal, 19452, 19786
-recovered Augustus_model.g40686.t1, internal, 19894, 19972
-recovered Augustus_model.g40686.t1, internal, 20180, 20325
-recovered Augustus_model.g40686.t1, internal, 20421, 20513
-recovered Augustus_model.g40686.t1, internal, 20648, 20701
-recovered Augustus_model.g40686.t1, internal, 20810, 20881
-recovered Augustus_model.g40686.t1, internal, 21003, 21029
-recovered Augustus_model.g40686.t1, internal, 21120, 21164
-recovered Augustus_model.g40686.t1, internal, 21431, 21484
-recovered Augustus_model.g40686.t1, internal, 21581, 21643
-recovered Augustus_model.g40686.t1, internal, 21802, 22022
-recovered Augustus_model.g40686.t1, internal, 22325, 22360
-recovered Augustus_model.g40686.t1, internal, 23170, 23232
-recovered Augustus_model.g40686.t1, internal, 24242, 24304
Valid prediction for GlimmerHMM_glimmerT_61161-T1
Couldn't classify 24911, 24970
Sorry, prediction pasa_asmbl_49449.p1 fails validation.
(ATG)	 AA	13816-13936	GT	AGG
(CCG)	 AG	16259-16870	GT	TGG
(TGA)	 AG	17096-17719	GT	CCG
(GAA)	 AG	17932-18531	GT	CAG
(ATC)	 AG	18698-19306	GT	AAG
(GCT)	 AG	19452-19786	GT	AGG
(GTT)	 AG	19894-19972	GT	AGG
(GTG)	 AG	20180-20325	GT	TGG
(GAC)	 AG	20421-20513	GT	AGG
(GGC)	 AG	20648-20701	GT	CTG
(GGA)	 AG	20810-20881	GT	AGG
(GGT)	 AG	21003-21029	GT	AGG
(GGA)	 AG	21120-21164	GT	AGG
(GGC)	 AG	21431-21484	GT	GGG
(GGT)	 AG	21581-21643	GT	CCG
(GGT)	 AG	21802-21867	GT	TGG
(GGA)	 AG	21969-22022	GT	GGG
(GGT)	 AG	22325-22360	GT	CTG
(GGA)	 AG	23170-23232	GT	GGG
(GGA)	 AG	24242-24304	GT	GGG
(GGC)	 AG	24911-24970	AA	GTA
-recovered pasa_asmbl_49449.p1, initial, 13816, 13936
-recovered pasa_asmbl_49449.p1, internal, 16259, 16870
-recovered pasa_asmbl_49449.p1, internal, 17096, 17719
-recovered pasa_asmbl_49449.p1, internal, 17932, 18531
-recovered pasa_asmbl_49449.p1, internal, 18698, 19306
-recovered pasa_asmbl_49449.p1, internal, 19452, 19786
-recovered pasa_asmbl_49449.p1, internal, 19894, 19972
-recovered pasa_asmbl_49449.p1, internal, 20180, 20325
-recovered pasa_asmbl_49449.p1, internal, 20421, 20513
-recovered pasa_asmbl_49449.p1, internal, 20648, 20701
-recovered pasa_asmbl_49449.p1, internal, 20810, 20881
-recovered pasa_asmbl_49449.p1, internal, 21003, 21029
-recovered pasa_asmbl_49449.p1, internal, 21120, 21164
-recovered pasa_asmbl_49449.p1, internal, 21431, 21484
-recovered pasa_asmbl_49449.p1, internal, 21581, 21643
-recovered pasa_asmbl_49449.p1, internal, 21802, 21867
-recovered pasa_asmbl_49449.p1, internal, 21969, 22022
-recovered pasa_asmbl_49449.p1, internal, 22325, 22360
-recovered pasa_asmbl_49449.p1, internal, 23170, 23232
-recovered pasa_asmbl_49449.p1, internal, 24242, 24304
Valid prediction for snap_scaffold_67-snap.4-T1
Couldn't classify 260, 564
Sorry, prediction GeneMark_model.106363_t fails validation.
(ACC)	 AG	260-564	GT	CAG
(ACT)	 AG	1257-1443	GT	AGG
(ACG)	 AG	1896-1933	GT	GAG
-recovered GeneMark_model.106363_t, terminal, 1896, 1933
-recovered GeneMark_model.106363_t, internal, 260, 564
-recovered GeneMark_model.106363_t, internal, 1257, 1443
-recovered GeneMark_model.106363_t, internal, 1896, 1933
Valid prediction for GeneMark_model.106362_t
Valid prediction for GlimmerHMM_glimmerT_61158-T1
Valid prediction for snap_scaffold_67-snap.3-T1
Valid prediction for snap_scaffold_67-snap.5-T1
Valid prediction for GlimmerHMM_glimmerT_61160-T1
Couldn't classify 116, 739
Sorry, prediction GlimmerHMM_glimmerT_61162-T1 fails validation.
(TGG)	 AG	116-739	GT	AGG
(TCA)	 AG	856-1443	GT	AGG
(TCC)	 AG	1577-2188	GT	AGG
(TGG)	 AG	4054-4653	GT	AGG
(ACG)	 AG	4875-5465	GT	GGG
(ATT)	 AG	6436-6656	GT	CTG
(CTG)	 AG	6736-6810	GA	AAG
add_exon() Sorry, GlimmerHMM_glimmerT_61162-T1 1577-2188-terminal-1 is invalid.
-recovered GlimmerHMM_glimmerT_61162-T1, terminal, 1577, 2188
-recovered GlimmerHMM_glimmerT_61162-T1, terminal, 6736, 6810
-recovered GlimmerHMM_glimmerT_61162-T1, internal, 116, 739
-recovered GlimmerHMM_glimmerT_61162-T1, internal, 856, 1443
-recovered GlimmerHMM_glimmerT_61162-T1, internal, 1577, 2188
-recovered GlimmerHMM_glimmerT_61162-T1, internal, 4054, 4653
-recovered GlimmerHMM_glimmerT_61162-T1, internal, 4875, 5465
-recovered GlimmerHMM_glimmerT_61162-T1, internal, 6436, 6656
Valid prediction for GlimmerHMM_glimmerT_61159-T1
Valid prediction for snap_scaffold_67-snap.8-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 25000
-exon list size: 105


building trellis

0.9    
1.9    
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6.5    
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13.1    
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20.6    
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22.4    
23.4    
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26.2    
27.1    
28.0    
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35.5    
36.4    
37.4    
38.3    
39.3    
40.2    
41.1    
42.1    
43.0    
43.9    
44.9    
45.8    
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48.6    
49.5    
50.5    
51.4    
52.3    
53.3    
54.2    
55.1    
56.1    
57.0    
57.9    
58.9    
59.8    
60.7    
61.7    
62.6    
63.6    
64.5    
65.4    
66.4    
67.3    
68.2    
69.2    
70.1    
71.0    
72.0    
72.9    
73.8    
74.8    
75.7    
76.6    
77.6    
78.5    
79.4    
80.4    
81.3    
82.2    
83.2    
84.1    
85.0    
86.0    
86.9    
87.9    
88.8    
89.7    
90.7    
91.6    
92.5    
93.5    
94.4    
95.3    
96.3    
97.2    
98.1    
99.1    
-found 5 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 4 predictions persist after filtering for low support