-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_60

-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_60-snap.1-T1
Valid prediction for HiQ_model.g39509.t1
Couldn't classify 5249, 5407
Couldn't classify 6272, 6319
Sorry, prediction pasa_asmbl_49455.p1 fails validation.
(GAC)	 GT	5249-5407	GT	TGG
(GGT)	 AG	5528-5608	GT	CAG
(GGT)	 AG	5767-5916	GT	GTG
(ATT)	 AG	6051-6128	GT	TGG
(GAT)	 AG	6272-6319	CA	GAC
-recovered pasa_asmbl_49455.p1, internal, 5528, 5608
-recovered pasa_asmbl_49455.p1, internal, 5767, 5916
-recovered pasa_asmbl_49455.p1, internal, 6051, 6128

-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_60-snap.2-T1
Valid prediction for Augustus_model.g39510.t1
Valid prediction for HiQ_model.g39511.t1
Couldn't classify 8880, 9017
Couldn't classify 9170, 9274
Sorry, prediction pasa_asmbl_49457.p1 fails validation.
(ATG)	 AA	5657-6037	GT	AGG
(CAG)	 AG	6331-6466	GT	GGG
(AGT)	 AG	6717-6871	GT	TAG
(GCA)	 AG	6953-7126	GT	ATG
(GTT)	 AG	7234-7356	GT	GAG
(GTG)	 AG	7778-8059	GT	TGG
(GCT)	 AG	8719-8772	GT	AGG
(GTT)	 AG	8880-9017	AT	AGA
(TTT)	 AC	9170-9274	GT	CGG
(AAC)	 AG	9575-9845	GT	AGG
(GTA)	 AG	9928-11234	CA	AAC
-recovered pasa_asmbl_49457.p1, initial, 5657, 6037
-recovered pasa_asmbl_49457.p1, terminal, 9928, 11234
-recovered pasa_asmbl_49457.p1, internal, 6331, 6466
-recovered pasa_asmbl_49457.p1, internal, 6717, 6871
-recovered pasa_asmbl_49457.p1, internal, 6953, 7126
-recovered pasa_asmbl_49457.p1, internal, 7234, 7356
-recovered pasa_asmbl_49457.p1, internal, 7778, 8059
-recovered pasa_asmbl_49457.p1, internal, 8719, 8772
-recovered pasa_asmbl_49457.p1, internal, 9575, 9845
Valid prediction for snap_scaffold_60-snap.4-T1
Valid prediction for snap_scaffold_60-snap.3-T1
Valid prediction for HiQ_model.g39512.t1
Couldn't classify 84, 210
Couldn't classify 2812, 2856
Sorry, prediction pasa_asmbl_49460.p1 fails validation.
(AGT)	 AG	84-210	GT	AGG
(ATT)	 AG	1601-1839	GT	TGG
(GTG)	 AG	2207-2380	GT	TGG
(CTG)	 AG	2812-2856	CT	TGC
-recovered pasa_asmbl_49460.p1, internal, 84, 210
-recovered pasa_asmbl_49460.p1, internal, 1601, 1839
-recovered pasa_asmbl_49460.p1, internal, 2207, 2380
Couldn't classify 84, 210
Sorry, prediction GlimmerHMM_glimmerT_59632-T1 fails validation.
(AGT)	 AG	84-210	GT	AGG
(ATT)	 AG	1601-1839	GT	TGG
(GTG)	 AG	2207-2380	GT	TGG
(CTG)	 AG	2812-3168	GT	TGG
(GTT)	 AG	5579-6037	GT	AGG
(GCA)	 AG	6334-6466	GT	GGG
(AGT)	 AG	6717-6871	GT	TAG
(GCA)	 AG	6953-7126	GT	ATG
(GTG)	 AG	7778-8036	GT	AGG
(GAG)	 AG	9177-9274	GT	CGG
(AAC)	 AG	9575-9845	GT	AGG
(GTA)	 AG	9928-11228	GT	TTG
(CTC)	 AG	16042-16095	GT	AGG
(GGC)	 AG	17001-17099	CA	AAC
add_exon() Sorry, GlimmerHMM_glimmerT_59632-T1 7778-8036-terminal-3 is invalid.
-recovered GlimmerHMM_glimmerT_59632-T1, terminal, 7778, 8036
-recovered GlimmerHMM_glimmerT_59632-T1, terminal, 17001, 17099
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 84, 210
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 1601, 1839
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 2207, 2380
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 2812, 3168
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 5579, 6037
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 6334, 6466
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 6717, 6871
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 6953, 7126
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 7778, 8036
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 9177, 9274
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 9575, 9845
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 9928, 11228
-recovered GlimmerHMM_glimmerT_59632-T1, internal, 16042, 16095

-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: 42


building trellis

2.3    
4.5    
6.8    
9.1    
11.4    
13.6    
15.9    
18.2    
20.5    
22.7    
25.0    
27.3    
29.5    
31.8    
34.1    
36.4    
38.6    
40.9    
43.2    
45.5    
47.7    
50.0    
52.3    
54.5    
56.8    
59.1    
61.4    
63.6    
65.9    
68.2    
70.5    
72.7    
75.0    
77.3    
79.5    
81.8    
84.1    
86.4    
88.6    
90.9    
93.2    
95.5    
97.7    
-found 4 predictions from path traversal
GOT 5prime partial gene.

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