-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_908

-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: +)Couldn't classify 2884, 3035
Sorry, prediction GlimmerHMM_glimmerT_62330-T1 fails validation.
(ATG)	 CT	1729-1829	GT	CTG
(CAT)	 AG	2193-2262	GT	GAG
(ACA)	 AG	2884-3035	GT	ACG
-recovered GlimmerHMM_glimmerT_62330-T1, initial, 1729, 1829
-recovered GlimmerHMM_glimmerT_62330-T1, internal, 2193, 2262
-recovered GlimmerHMM_glimmerT_62330-T1, internal, 2884, 3035
Couldn't classify 2888, 3035
Sorry, prediction GeneMark_model.108591_t fails validation.
(ATG)	 CT	1729-1759	GT	CTG
(TGG)	 AG	1812-1829	GT	CTG
(TGG)	 AG	1936-1964	GT	CTG
(GGG)	 AG	2252-2262	GT	GAG
(TTC)	 AG	2297-2325	GT	CTG
(TGG)	 AG	2354-2371	GT	CTG
(TGG)	 AG	2400-2417	GT	CTG
(TGG)	 AG	2470-2487	GT	CTG
(TGG)	 AG	2516-2533	GT	CTG
(TGG)	 AG	2562-2579	GT	CTG
(TGG)	 AG	2608-2625	GT	CTG
(TGG)	 AG	2678-2695	GT	CTG
(TGG)	 AG	2724-2741	GT	CTG
(TGG)	 AG	2770-2787	GT	CTG
(CAG)	 AG	2888-3035	GT	ACG
-recovered GeneMark_model.108591_t, initial, 1729, 1759
-recovered GeneMark_model.108591_t, internal, 1812, 1829
-recovered GeneMark_model.108591_t, internal, 1936, 1964
-recovered GeneMark_model.108591_t, internal, 2252, 2262
-recovered GeneMark_model.108591_t, internal, 2297, 2325
-recovered GeneMark_model.108591_t, internal, 2354, 2371
-recovered GeneMark_model.108591_t, internal, 2400, 2417
-recovered GeneMark_model.108591_t, internal, 2470, 2487
-recovered GeneMark_model.108591_t, internal, 2516, 2533
-recovered GeneMark_model.108591_t, internal, 2562, 2579
-recovered GeneMark_model.108591_t, internal, 2608, 2625
-recovered GeneMark_model.108591_t, internal, 2678, 2695
-recovered GeneMark_model.108591_t, internal, 2724, 2741
-recovered GeneMark_model.108591_t, internal, 2770, 2787
-recovered GeneMark_model.108591_t, internal, 2888, 3035
Couldn't classify 2888, 3035
Sorry, prediction snap_scaffold_908-snap.2-T1 fails validation.
(ATG)	 CT	2387-2471	GT	TGG
(CAG)	 AG	2888-3035	GT	ACG
-recovered snap_scaffold_908-snap.2-T1, initial, 2387, 2471
-recovered snap_scaffold_908-snap.2-T1, internal, 2888, 3035
Couldn't classify 32, 94
Sorry, prediction snap_scaffold_908-snap.1-T1 fails validation.
(AAG)	 AG	32-94	GT	TGG
(AAA)	 AG	616-896	GT	AGG
(GTA)	 AG	1245-1379	AA	GAA
-recovered snap_scaffold_908-snap.1-T1, terminal, 1245, 1379
-recovered snap_scaffold_908-snap.1-T1, internal, 32, 94
-recovered snap_scaffold_908-snap.1-T1, internal, 616, 896
Couldn't classify 1, 94
Sorry, prediction Augustus_model.g41433.t1 fails validation.
(TAT)	 CT	1-94	GT	TGG
(AAA)	 AG	616-732	GT	GGG
(AGG)	 AG	850-896	GT	AGG
(GTA)	 AG	1245-1379	AA	GAA
-recovered Augustus_model.g41433.t1, terminal, 1245, 1379
-recovered Augustus_model.g41433.t1, internal, 616, 732
-recovered Augustus_model.g41433.t1, internal, 850, 896
Couldn't classify 20, 94
Sorry, prediction GeneMark_model.108590_t fails validation.
(AGA)	 AG	20-94	GT	TGG
(AAA)	 AG	616-732	GT	GGG
(AGG)	 AG	850-896	GT	AGG
(GTA)	 AG	1245-1379	AA	GAA
-recovered GeneMark_model.108590_t, terminal, 1245, 1379
-recovered GeneMark_model.108590_t, internal, 20, 94
-recovered GeneMark_model.108590_t, internal, 616, 732
-recovered GeneMark_model.108590_t, internal, 850, 896

-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 Augustus_model.g41434.t1

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

-building trellis in range 1 - 4000
-exon list size: 46


building trellis

2.1    
4.2    
6.2    
8.3    
10.4    
12.5    
14.6    
16.7    
18.8    
20.8    
22.9    
25.0    
27.1    
29.2    
31.2    
33.3    
35.4    
37.5    
39.6    
41.7    
43.8    
45.8    
47.9    
50.0    
52.1    
54.2    
56.2    
58.3    
60.4    
62.5    
64.6    
66.7    
68.8    
70.8    
72.9    
75.0    
77.1    
79.2    
81.2    
83.3    
85.4    
87.5    
89.6    
91.7    
93.8    
95.8    
97.9    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support