-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/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.6-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 CodingQuarry_transcript_55504-T1
Valid prediction for snap_scaffold_67-snap.2-T1
Couldn't classify 116, 739
Sorry, prediction GlimmerHMM_glimmerT_59666-T1 fails validation.
(TGG)	 AG	116-739	GT	AGG
(TCA)	 AG	856-1443	GT	AGG
(TCC)	 AG	1577-2188	GT	AGG
(CTG)	 AG	2772-3436	TT	AGT
add_exon() Sorry, GlimmerHMM_glimmerT_59666-T1 1577-2188-terminal-1 is invalid.
-recovered GlimmerHMM_glimmerT_59666-T1, terminal, 1577, 2188
-recovered GlimmerHMM_glimmerT_59666-T1, terminal, 2772, 3436
-recovered GlimmerHMM_glimmerT_59666-T1, internal, 116, 739
-recovered GlimmerHMM_glimmerT_59666-T1, internal, 856, 1443
-recovered GlimmerHMM_glimmerT_59666-T1, internal, 1577, 2188
Couldn't classify 13040, 13085
Couldn't classify 24911, 24973
Sorry, prediction pasa_asmbl_49511.p1 fails validation.
(GAG)	 AG	13040-13085	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	21802-21867	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	24911-24973	GT	AGG
add_exon() Sorry, pasa_asmbl_49511.p1 13355-13936-terminal-1 is invalid.
-recovered pasa_asmbl_49511.p1, terminal, 13355, 13936
-recovered pasa_asmbl_49511.p1, internal, 13040, 13085
-recovered pasa_asmbl_49511.p1, internal, 13355, 13936
-recovered pasa_asmbl_49511.p1, internal, 16259, 16870
-recovered pasa_asmbl_49511.p1, internal, 17096, 17719
-recovered pasa_asmbl_49511.p1, internal, 17932, 18531
-recovered pasa_asmbl_49511.p1, internal, 18698, 19306
-recovered pasa_asmbl_49511.p1, internal, 19452, 19786
-recovered pasa_asmbl_49511.p1, internal, 19894, 19972
-recovered pasa_asmbl_49511.p1, internal, 20180, 20325
-recovered pasa_asmbl_49511.p1, internal, 20421, 20513
-recovered pasa_asmbl_49511.p1, internal, 20648, 20701
-recovered pasa_asmbl_49511.p1, internal, 20810, 20881
-recovered pasa_asmbl_49511.p1, internal, 21003, 21029
-recovered pasa_asmbl_49511.p1, internal, 21120, 21164
-recovered pasa_asmbl_49511.p1, internal, 21431, 21484
-recovered pasa_asmbl_49511.p1, internal, 21581, 21643
-recovered pasa_asmbl_49511.p1, internal, 21802, 21867
-recovered pasa_asmbl_49511.p1, internal, 21969, 22022
-recovered pasa_asmbl_49511.p1, internal, 22325, 22360
-recovered pasa_asmbl_49511.p1, internal, 23170, 23232
-recovered pasa_asmbl_49511.p1, internal, 24242, 24304
-recovered pasa_asmbl_49511.p1, internal, 24911, 24973
Couldn't classify 972, 1412
Sorry, prediction pasa_asmbl_49513.p1 fails validation.
(ATG)	 GA	972-1412	AA	CCA
Couldn't classify 116, 739
Couldn't classify 24911, 25000
Sorry, prediction Augustus_model.g39535.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
(CAT)	 AG	8438-8511	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	21802-21867	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	24911-25000		TG
add_exon() Sorry, Augustus_model.g39535.t1 1577-2188-terminal-1 is invalid.
-recovered Augustus_model.g39535.t1, terminal, 1577, 2188
add_exon() Sorry, Augustus_model.g39535.t1 8438-8511-terminal-2 is invalid.
-recovered Augustus_model.g39535.t1, terminal, 8438, 8511
add_exon() Sorry, Augustus_model.g39535.t1 13355-13936-terminal-1 is invalid.
-recovered Augustus_model.g39535.t1, terminal, 13355, 13936
-recovered Augustus_model.g39535.t1, internal, 116, 739
-recovered Augustus_model.g39535.t1, internal, 856, 1443
-recovered Augustus_model.g39535.t1, internal, 1577, 2188
-recovered Augustus_model.g39535.t1, internal, 2823, 3112
-recovered Augustus_model.g39535.t1, internal, 4970, 5234
-recovered Augustus_model.g39535.t1, internal, 6436, 6703
-recovered Augustus_model.g39535.t1, internal, 8438, 8511
-recovered Augustus_model.g39535.t1, internal, 8750, 9043
-recovered Augustus_model.g39535.t1, internal, 9656, 10015
-recovered Augustus_model.g39535.t1, internal, 10530, 10621
-recovered Augustus_model.g39535.t1, internal, 10825, 10891
-recovered Augustus_model.g39535.t1, internal, 12507, 13085
-recovered Augustus_model.g39535.t1, internal, 13355, 13936
-recovered Augustus_model.g39535.t1, internal, 16259, 16870
-recovered Augustus_model.g39535.t1, internal, 17096, 17719
-recovered Augustus_model.g39535.t1, internal, 17932, 18531
-recovered Augustus_model.g39535.t1, internal, 18698, 19306
-recovered Augustus_model.g39535.t1, internal, 19452, 19786
-recovered Augustus_model.g39535.t1, internal, 19894, 19972
-recovered Augustus_model.g39535.t1, internal, 20180, 20325
-recovered Augustus_model.g39535.t1, internal, 20421, 20513
-recovered Augustus_model.g39535.t1, internal, 20648, 20701
-recovered Augustus_model.g39535.t1, internal, 20810, 20881
-recovered Augustus_model.g39535.t1, internal, 21003, 21029
-recovered Augustus_model.g39535.t1, internal, 21120, 21164
-recovered Augustus_model.g39535.t1, internal, 21431, 21484
-recovered Augustus_model.g39535.t1, internal, 21581, 21643
-recovered Augustus_model.g39535.t1, internal, 21802, 21867
-recovered Augustus_model.g39535.t1, internal, 21969, 22022
-recovered Augustus_model.g39535.t1, internal, 22325, 22360
-recovered Augustus_model.g39535.t1, internal, 23170, 23232
-recovered Augustus_model.g39535.t1, internal, 24242, 24304
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 GlimmerHMM_glimmerT_59662-T1
Valid prediction for GlimmerHMM_glimmerT_59663-T1
Valid prediction for snap_scaffold_67-snap.7-T1
Valid prediction for snap_scaffold_67-snap.3-T1
Valid prediction for snap_scaffold_67-snap.5-T1
Valid prediction for snap_scaffold_67-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_59665-T1
Valid prediction for GlimmerHMM_glimmerT_59664-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: 86


building trellis

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2.3    
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8.0    
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14.8    
15.9    
17.0    
18.2    
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23.9    
25.0    
26.1    
27.3    
28.4    
29.5    
30.7    
31.8    
33.0    
34.1    
35.2    
36.4    
37.5    
38.6    
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40.9    
42.0    
43.2    
44.3    
45.5    
46.6    
47.7    
48.9    
50.0    
51.1    
52.3    
53.4    
54.5    
55.7    
56.8    
58.0    
59.1    
60.2    
61.4    
62.5    
63.6    
64.8    
65.9    
67.0    
68.2    
69.3    
70.5    
71.6    
72.7    
73.9    
75.0    
76.1    
77.3    
78.4    
79.5    
80.7    
81.8    
83.0    
84.1    
85.2    
86.4    
87.5    
88.6    
89.8    
90.9    
92.0    
93.2    
94.3    
95.5    
96.6    
97.7    
98.9    
-found 3 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support