-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_73

-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 HiQ_model.g39553.t1
Valid prediction for snap_scaffold_73-snap.3-T1
Valid prediction for snap_scaffold_73-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 snap_scaffold_73-snap.4-T1
Valid prediction for snap_scaffold_73-snap.1-T1
Valid prediction for snap_scaffold_73-snap.5-T1
Valid prediction for Augustus_model.g39554.t1
Valid prediction for Augustus_model.g39552.t1
Valid prediction for Augustus_model.g39555.t1
Couldn't classify 6646, 6660
Couldn't classify 7417, 7847
Sorry, prediction pasa_asmbl_51628.p1 fails validation.
(CTC)	 GC	6646-6660	GT	AGG
(GAG)	 AG	6751-6888	GT	AGG
(GGC)	 AG	6999-7050	GT	AGG
(TGG)	 AG	7140-7166	GT	AGG
(TTT)	 AG	7251-7277	GT	AGG
(ATG)	 AG	7417-7847	AA	AGA
-recovered pasa_asmbl_51628.p1, internal, 6751, 6888
-recovered pasa_asmbl_51628.p1, internal, 6999, 7050
-recovered pasa_asmbl_51628.p1, internal, 7140, 7166
-recovered pasa_asmbl_51628.p1, internal, 7251, 7277
Valid prediction for GlimmerHMM_glimmerT_59693-T1
Couldn't classify 1531, 1617
Sorry, prediction GlimmerHMM_glimmerT_59694-T1 fails validation.
(GGA)	 AG	1531-1617	GT	AGG
(TTC)	 AG	1709-1795	GT	AAG
(ATA)	 AG	2006-2125	GT	AGG
(GAG)	 AG	2216-2353	GT	AGG
(GGC)	 AG	2464-2515	GT	AGG
(ATG)	 AG	2882-3369	GT	CGG
(GGA)	 AG	6066-6152	GT	AGG
(ATG)	 AG	6541-6660	GT	AGG
(GAG)	 AG	6751-6888	GT	AGG
(GGC)	 AG	6999-7050	GT	AGG
(ATG)	 AG	7417-7955	AT	GAA
add_exon() Sorry, GlimmerHMM_glimmerT_59694-T1 2882-3369-initial-1 is invalid.
-recovered GlimmerHMM_glimmerT_59694-T1, initial, 2882, 3369
-recovered GlimmerHMM_glimmerT_59694-T1, initial, 6541, 6660
-recovered GlimmerHMM_glimmerT_59694-T1, terminal, 7417, 7955
-recovered GlimmerHMM_glimmerT_59694-T1, internal, 1531, 1617
-recovered GlimmerHMM_glimmerT_59694-T1, internal, 1709, 1795
-recovered GlimmerHMM_glimmerT_59694-T1, internal, 2006, 2125
-recovered GlimmerHMM_glimmerT_59694-T1, internal, 2216, 2353
-recovered GlimmerHMM_glimmerT_59694-T1, internal, 2464, 2515
-recovered GlimmerHMM_glimmerT_59694-T1, internal, 2882, 3369
-recovered GlimmerHMM_glimmerT_59694-T1, internal, 6066, 6152
-recovered GlimmerHMM_glimmerT_59694-T1, internal, 6541, 6660
-recovered GlimmerHMM_glimmerT_59694-T1, internal, 6751, 6888
-recovered GlimmerHMM_glimmerT_59694-T1, internal, 6999, 7050
Valid prediction for Augustus_model.g39556.t1
Valid prediction for snap_scaffold_73-snap.7-T1
Valid prediction for snap_scaffold_73-snap.2-T1
Couldn't classify 2084, 2125
Sorry, prediction pasa_asmbl_51629.p1 fails validation.
(CAA)	 GC	2084-2125	GT	AGG
(GAG)	 AG	2216-2353	GT	AGG
(GGC)	 AG	2464-2515	GT	AGG
(TGG)	 AG	2605-2631	GT	AGG
(TTT)	 AG	2716-2742	GT	AGG
(ATG)	 AG	2882-3420	AT	GAA
-recovered pasa_asmbl_51629.p1, terminal, 2882, 3420
-recovered pasa_asmbl_51629.p1, internal, 2216, 2353
-recovered pasa_asmbl_51629.p1, internal, 2464, 2515
-recovered pasa_asmbl_51629.p1, internal, 2605, 2631
-recovered pasa_asmbl_51629.p1, internal, 2716, 2742

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

-building trellis in range 1 - 24028
-exon list size: 55


building trellis

1.8    
3.5    
5.3    
7.0    
8.8    
10.5    
12.3    
14.0    
15.8    
17.5    
19.3    
21.1    
22.8    
24.6    
26.3    
28.1    
29.8    
31.6    
33.3    
35.1    
36.8    
38.6    
40.4    
42.1    
43.9    
45.6    
47.4    
49.1    
50.9    
52.6    
54.4    
56.1    
57.9    
59.6    
61.4    
63.2    
64.9    
66.7    
68.4    
70.2    
71.9    
73.7    
75.4    
77.2    
78.9    
80.7    
82.5    
84.2    
86.0    
87.7    
89.5    
91.2    
93.0    
94.7    
96.5    
98.2    
-found 7 predictions from path traversal
GOT 5prime partial gene.

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