-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_730

-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 377, 418
Sorry, prediction GeneMark_model.108269_t fails validation.
(GGC)	 AG	377-418	GT	TCG
(GTC)	 AG	537-578	GT	TCG
(GGC)	 AG	601-642	GT	TGG
(GGT)	 AG	665-706	GT	AGG
(AGG)	 AG	839-850	GT	TCG
(AGG)	 AG	871-882	GT	CGG
(GTC)	 AG	905-946	GT	TTG
(AGG)	 AG	967-978	GT	AGG
(GGC)	 AG	1001-1042	GT	TGG
(GTC)	 AG	1065-1106	GT	AGG
(GGC)	 AG	1145-1186	GT	TGG
(GGC)	 AG	1209-1214	GT	GTG
(AAG)	 AG	1239-1250	GT	AGG
(GGC)	 AG	1289-1330	GT	TCG
(AGG)	 AG	1351-1362	GT	TGG
(GGC)	 AG	1385-1426	GT	TCG
(AGG)	 AG	1447-1458	GT	TGG
(GGC)	 AG	1481-1522	GT	TCG
(GTC)	 AG	1545-1586	GT	AGG
(GTC)	 AG	1609-1650	GT	AGG
(GGT)	 AG	1760-1790	TG	AAT
add_exon() Sorry, GeneMark_model.108269_t 665-706-terminal-1 is invalid.
-recovered GeneMark_model.108269_t, terminal, 665, 706
-recovered GeneMark_model.108269_t, terminal, 967, 978
add_exon() Sorry, GeneMark_model.108269_t 1065-1106-terminal-1 is invalid.
-recovered GeneMark_model.108269_t, terminal, 1065, 1106
-recovered GeneMark_model.108269_t, terminal, 1239, 1250
add_exon() Sorry, GeneMark_model.108269_t 1545-1586-terminal-1 is invalid.
-recovered GeneMark_model.108269_t, terminal, 1545, 1586
add_exon() Sorry, GeneMark_model.108269_t 1609-1650-terminal-1 is invalid.
-recovered GeneMark_model.108269_t, terminal, 1609, 1650
-recovered GeneMark_model.108269_t, terminal, 1760, 1790
-recovered GeneMark_model.108269_t, internal, 377, 418
-recovered GeneMark_model.108269_t, internal, 537, 578
-recovered GeneMark_model.108269_t, internal, 601, 642
-recovered GeneMark_model.108269_t, internal, 665, 706
-recovered GeneMark_model.108269_t, internal, 839, 850
-recovered GeneMark_model.108269_t, internal, 871, 882
-recovered GeneMark_model.108269_t, internal, 905, 946
-recovered GeneMark_model.108269_t, internal, 967, 978
-recovered GeneMark_model.108269_t, internal, 1001, 1042
-recovered GeneMark_model.108269_t, internal, 1065, 1106
-recovered GeneMark_model.108269_t, internal, 1145, 1186
-recovered GeneMark_model.108269_t, internal, 1209, 1214
-recovered GeneMark_model.108269_t, internal, 1239, 1250
-recovered GeneMark_model.108269_t, internal, 1289, 1330
-recovered GeneMark_model.108269_t, internal, 1351, 1362
-recovered GeneMark_model.108269_t, internal, 1385, 1426
-recovered GeneMark_model.108269_t, internal, 1447, 1458
-recovered GeneMark_model.108269_t, internal, 1481, 1522
-recovered GeneMark_model.108269_t, internal, 1545, 1586
-recovered GeneMark_model.108269_t, internal, 1609, 1650

-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_730-snap.1-T1
Couldn't classify 241, 255
Sorry, prediction GeneMark_model.108270_t fails validation.
(GAG)	 AG	241-255	GT	AAG
(GAA)	 AG	408-434	GT	GGG
(GTT)	 AG	522-551	GT	GGG
(CGT)	 AG	595-796	GT	TCG
(GGA)	 AG	1084-1138	GT	ACG
(AGA)	 AG	2350-2545	GT	AAG
(GCA)	 AG	2569-2590	AC	AGA
-recovered GeneMark_model.108270_t, terminal, 2569, 2590
-recovered GeneMark_model.108270_t, internal, 241, 255
-recovered GeneMark_model.108270_t, internal, 408, 434
-recovered GeneMark_model.108270_t, internal, 522, 551
-recovered GeneMark_model.108270_t, internal, 595, 796
-recovered GeneMark_model.108270_t, internal, 1084, 1138
-recovered GeneMark_model.108270_t, internal, 2350, 2545
Valid prediction for GlimmerHMM_glimmerT_62172-T1
Valid prediction for snap_scaffold_730-snap.2-T1
Valid prediction for Augustus_model.g41325.t1

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

-building trellis in range 1 - 4769
-exon list size: 57


building trellis

1.7    
3.4    
5.1    
6.8    
8.5    
10.2    
11.9    
13.6    
15.3    
16.9    
18.6    
20.3    
22.0    
23.7    
25.4    
27.1    
28.8    
30.5    
32.2    
33.9    
35.6    
37.3    
39.0    
40.7    
42.4    
44.1    
45.8    
47.5    
49.2    
50.8    
52.5    
54.2    
55.9    
57.6    
59.3    
61.0    
62.7    
64.4    
66.1    
67.8    
69.5    
71.2    
72.9    
74.6    
76.3    
78.0    
79.7    
81.4    
83.1    
84.7    
86.4    
88.1    
89.8    
91.5    
93.2    
94.9    
96.6    
98.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support