-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_548

-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_61976-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61976-T1 4637-4935-terminal-1 is invalid.
Couldn't classify 4181, 4278
Sorry, prediction snap_scaffold_548-snap.1-T1 fails validation.
(ATG)	 CG	3905-4006	GT	CAG
(GCC)	 AG	4181-4278	GT	AGG
-recovered snap_scaffold_548-snap.1-T1, initial, 3905, 4006
-recovered snap_scaffold_548-snap.1-T1, internal, 4181, 4278

-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: -)Couldn't classify 387, 454
Sorry, prediction GlimmerHMM_glimmerT_61977-T1 fails validation.
(GGG)	 AG	387-454	GT	AAG
(CAC)	 AG	551-613	AG	GAA
-recovered GlimmerHMM_glimmerT_61977-T1, terminal, 551, 613
-recovered GlimmerHMM_glimmerT_61977-T1, internal, 387, 454
Couldn't classify 10, 126
Sorry, prediction GeneMark_model.107912_t fails validation.
(GAG)	 AG	10-126	GT	ATG
(GGT)	 AG	406-454	GT	AAG
(GTG)	 AG	866-894	GT	AGG
(GGC)	 AG	916-1024	GT	AGG
(GTG)	 AG	1060-1088	GT	AGG
(AGC)	 AG	1112-1121	GT	AGG
(GTG)	 AG	1157-1187	GT	AGG
(GTG)	 AG	1258-1285	GT	AGG
(AGA)	 AG	1308-1319	GT	AGG
(AAG)	 AG	1340-1360	GT	AGG
(GGG)	 AG	1392-1460	GT	AGG
(GCT)	 AG	1483-1527	GT	AGG
(AGA)	 AG	1549-1573	GT	AGG
(GTT)	 AG	1633-1643	GT	AGG
(AGA)	 AG	1665-1671	TG	GAT
-recovered GeneMark_model.107912_t, terminal, 1665, 1671
-recovered GeneMark_model.107912_t, internal, 10, 126
-recovered GeneMark_model.107912_t, internal, 406, 454
-recovered GeneMark_model.107912_t, internal, 866, 894
-recovered GeneMark_model.107912_t, internal, 916, 1024
-recovered GeneMark_model.107912_t, internal, 1060, 1088
-recovered GeneMark_model.107912_t, internal, 1112, 1121
-recovered GeneMark_model.107912_t, internal, 1157, 1187
-recovered GeneMark_model.107912_t, internal, 1258, 1285
-recovered GeneMark_model.107912_t, internal, 1308, 1319
-recovered GeneMark_model.107912_t, internal, 1340, 1360
-recovered GeneMark_model.107912_t, internal, 1392, 1460
-recovered GeneMark_model.107912_t, internal, 1483, 1527
-recovered GeneMark_model.107912_t, internal, 1549, 1573
-recovered GeneMark_model.107912_t, internal, 1633, 1643
Couldn't classify 5862, 5921
Sorry, prediction GeneMark_model.107911_t fails validation.
(ATG)	 GT	3277-3281	GT	GTG
(AAG)	 AG	5616-5654	GT	GAG
(AGA)	 AG	5690-5788	GT	GAG
(AGA)	 AG	5810-5824	GT	GAG
(AGA)	 AG	5862-5921	GT	GAG
-recovered GeneMark_model.107911_t, initial, 3277, 3281
-recovered GeneMark_model.107911_t, internal, 5616, 5654
-recovered GeneMark_model.107911_t, internal, 5690, 5788
-recovered GeneMark_model.107911_t, internal, 5810, 5824
-recovered GeneMark_model.107911_t, internal, 5862, 5921

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

-building trellis in range 1 - 5960
-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 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support