-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_39

-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 GlimmerHMM_glimmerT_59530-T1
Valid prediction for Augustus_model.g39429.t1
Valid prediction for snap_scaffold_39-snap.4-T1
Valid prediction for snap_scaffold_39-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_59532-T1
Valid prediction for Augustus_model.g39430.t1
Valid prediction for GlimmerHMM_glimmerT_59531-T1
Valid prediction for GlimmerHMM_glimmerT_59534-T1
Valid prediction for CodingQuarry_transcript_46581-T1
Valid prediction for pasa_asmbl_41063.p1

-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_46582-T1
Couldn't classify 34586, 34648
Couldn't classify 35754, 35818
Sorry, prediction pasa_asmbl_41067.p1 fails validation.
(CCC)	 TG	34586-34648	GT	AGG
(GTT)	 AG	34736-34885	GT	CTG
(GTA)	 AG	35018-35233	GT	AAG
(GAT)	 AG	35424-35523	GT	TGG
(AAA)	 AG	35754-35818	TG	CCT
-recovered pasa_asmbl_41067.p1, internal, 34736, 34885
-recovered pasa_asmbl_41067.p1, internal, 35018, 35233
-recovered pasa_asmbl_41067.p1, internal, 35424, 35523
Valid prediction for GlimmerHMM_glimmerT_59527-T1
Valid prediction for snap_scaffold_39-snap.6-T1
Valid prediction for snap_scaffold_39-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_59533-T1
Couldn't classify 35424, 35456
Sorry, prediction snap_scaffold_39-snap.1-T1 fails validation.
(ATG)	 AC	29479-29655	GT	AGG
(TTT)	 AG	30208-30276	GT	TAG
(GTC)	 AG	30635-30791	GT	GAG
(TCC)	 AG	30874-30926	GT	TGG
(TTT)	 AG	31287-31307	GT	AGG
(GAC)	 AG	31858-32026	GT	CGG
(TCC)	 AG	32130-32214	GT	AAG
(GTA)	 AG	32315-32428	GT	AAG
(AGG)	 AG	33042-33077	GT	CGG
(ATC)	 AG	33387-33495	GT	CAG
(ATC)	 AG	33517-33669	GT	ATG
(GCT)	 AG	33848-34084	GT	TGG
(GTG)	 AG	34344-34407	GT	AGG
(TAA)	 AG	34503-34648	GT	AGG
(GTT)	 AG	34736-34885	GT	CTG
(GTA)	 AG	35018-35233	GT	AAG
(GAT)	 AG	35424-35456	GT	AGG
-recovered snap_scaffold_39-snap.1-T1, initial, 29479, 29655
-recovered snap_scaffold_39-snap.1-T1, internal, 30208, 30276
-recovered snap_scaffold_39-snap.1-T1, internal, 30635, 30791
-recovered snap_scaffold_39-snap.1-T1, internal, 30874, 30926
-recovered snap_scaffold_39-snap.1-T1, internal, 31287, 31307
-recovered snap_scaffold_39-snap.1-T1, internal, 31858, 32026
-recovered snap_scaffold_39-snap.1-T1, internal, 32130, 32214
-recovered snap_scaffold_39-snap.1-T1, internal, 32315, 32428
-recovered snap_scaffold_39-snap.1-T1, internal, 33042, 33077
-recovered snap_scaffold_39-snap.1-T1, internal, 33387, 33495
-recovered snap_scaffold_39-snap.1-T1, internal, 33517, 33669
-recovered snap_scaffold_39-snap.1-T1, internal, 33848, 34084
-recovered snap_scaffold_39-snap.1-T1, internal, 34344, 34407
-recovered snap_scaffold_39-snap.1-T1, internal, 34503, 34648
-recovered snap_scaffold_39-snap.1-T1, internal, 34736, 34885
-recovered snap_scaffold_39-snap.1-T1, internal, 35018, 35233
-recovered snap_scaffold_39-snap.1-T1, internal, 35424, 35456
Valid prediction for Augustus_model.g39431.t1
Valid prediction for GlimmerHMM_glimmerT_59529-T1
Valid prediction for Augustus_model.g39428.t1
Valid prediction for Augustus_model.g39432.t1
Couldn't classify 35754, 35820
Sorry, prediction Augustus_model.g39427.t1 fails validation.
(ATG)	 TG	28859-28893	GT	TCG
(TAT)	 AG	29472-29655	GT	AGG
(TTT)	 AG	30208-30300	GT	AGG
(GTC)	 AG	30635-30791	GT	GAG
(TCC)	 AG	30874-30926	GT	TGG
(TTT)	 AG	31287-31307	GT	AGG
(GAC)	 AG	31858-32026	GT	CGG
(TCC)	 AG	32130-32214	GT	AAG
(GTA)	 AG	32315-32441	GT	CTG
(ATC)	 AG	33517-33681	GT	AGG
(GCT)	 AG	33848-34084	GT	TGG
(GTG)	 AG	34344-34407	GT	AGG
(TAA)	 AG	34503-34648	GT	AGG
(GTT)	 AG	34736-34885	GT	CTG
(GTA)	 AG	35018-35233	GT	AAG
(GAT)	 AG	35424-35523	GT	TGG
(AAA)	 AG	35754-35820		TG
-recovered Augustus_model.g39427.t1, initial, 28859, 28893
-recovered Augustus_model.g39427.t1, internal, 29472, 29655
-recovered Augustus_model.g39427.t1, internal, 30208, 30300
-recovered Augustus_model.g39427.t1, internal, 30635, 30791
-recovered Augustus_model.g39427.t1, internal, 30874, 30926
-recovered Augustus_model.g39427.t1, internal, 31287, 31307
-recovered Augustus_model.g39427.t1, internal, 31858, 32026
-recovered Augustus_model.g39427.t1, internal, 32130, 32214
-recovered Augustus_model.g39427.t1, internal, 32315, 32441
-recovered Augustus_model.g39427.t1, internal, 33517, 33681
-recovered Augustus_model.g39427.t1, internal, 33848, 34084
-recovered Augustus_model.g39427.t1, internal, 34344, 34407
-recovered Augustus_model.g39427.t1, internal, 34503, 34648
-recovered Augustus_model.g39427.t1, internal, 34736, 34885
-recovered Augustus_model.g39427.t1, internal, 35018, 35233
-recovered Augustus_model.g39427.t1, internal, 35424, 35523
Valid prediction for pasa_asmbl_41071.p1
Valid prediction for snap_scaffold_39-snap.8-T1
add_exon() Sorry, snap_scaffold_39-snap.8-T1 1880-2100-terminal-1 is invalid.
Valid prediction for snap_scaffold_39-snap.5-T1
Valid prediction for snap_scaffold_39-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_59528-T1

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

-building trellis in range 1 - 35820
-exon list size: 87


building trellis

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6.7    
7.9    
9.0    
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16.9    
18.0    
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25.8    
27.0    
28.1    
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30.3    
31.5    
32.6    
33.7    
34.8    
36.0    
37.1    
38.2    
39.3    
40.4    
41.6    
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44.9    
46.1    
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51.7    
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53.9    
55.1    
56.2    
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58.4    
59.6    
60.7    
61.8    
62.9    
64.0    
65.2    
66.3    
67.4    
68.5    
69.7    
70.8    
71.9    
73.0    
74.2    
75.3    
76.4    
77.5    
78.7    
79.8    
80.9    
82.0    
83.1    
84.3    
85.4    
86.5    
87.6    
88.8    
89.9    
91.0    
92.1    
93.3    
94.4    
95.5    
96.6    
97.8    
98.9    
-found 8 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 6 predictions persist after filtering for low support