-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_860

-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 2110, 3265
Couldn't classify 3407, 3609
Sorry, prediction snap_scaffold_860-snap.1-T1 fails validation.
(AGG)	 AG	2110-3265	GT	AAG
(ATA)	 AG	3407-3609	GT	AAG
add_exon() Sorry, snap_scaffold_860-snap.1-T1 2110-3265-terminal-3 is invalid.
-recovered snap_scaffold_860-snap.1-T1, terminal, 2110, 3265
-recovered snap_scaffold_860-snap.1-T1, internal, 2110, 3265
-recovered snap_scaffold_860-snap.1-T1, internal, 3407, 3609
Valid prediction for GlimmerHMM_glimmerT_62296-T1
Valid prediction for GeneMark_model.108506_t
Couldn't classify 129, 242
Sorry, prediction GeneMark_model.108505_t fails validation.
(AAA)	 AG	129-242	GT	ACG
(AGA)	 AG	269-304	GT	ACG
(AGA)	 AG	325-378	GT	ACG
(AGA)	 AG	401-412	GT	ACG
(ACA)	 AG	439-592	GT	TGG
(AGA)	 AG	720-808	GC	GAG
(GAG)	 AG	836-985	GT	AGG
(AGA)	 AG	1009-1108	GT	TAG
(CAC)	 AG	1323-1336	GT	CTG
(ACG)	 AG	1455-1460	GC	GAG
(AGG)	 AG	1482-1538	GT	AGG
(AGC)	 AG	1577-1585	GT	GTG
(AGA)	 AG	1609-1641	GT	GGG
(AGG)	 AG	1676-1687	GT	AGG
(AGA)	 AG	1715-1744	GT	AGG
(AGA)	 AG	1791-1796	GT	AGG
(AGA)	 AG	1823-1838	AG	AAA
-recovered GeneMark_model.108505_t, terminal, 1823, 1838
-recovered GeneMark_model.108505_t, internal, 129, 242
-recovered GeneMark_model.108505_t, internal, 269, 304
-recovered GeneMark_model.108505_t, internal, 325, 378
-recovered GeneMark_model.108505_t, internal, 401, 412
-recovered GeneMark_model.108505_t, internal, 439, 592
-recovered GeneMark_model.108505_t, internal, 720, 808
-recovered GeneMark_model.108505_t, internal, 836, 985
-recovered GeneMark_model.108505_t, internal, 1009, 1108
-recovered GeneMark_model.108505_t, internal, 1323, 1336
-recovered GeneMark_model.108505_t, internal, 1455, 1460
-recovered GeneMark_model.108505_t, internal, 1482, 1538
-recovered GeneMark_model.108505_t, internal, 1577, 1585
-recovered GeneMark_model.108505_t, internal, 1609, 1641
-recovered GeneMark_model.108505_t, internal, 1676, 1687
-recovered GeneMark_model.108505_t, internal, 1715, 1744
-recovered GeneMark_model.108505_t, internal, 1791, 1796
Valid prediction for Augustus_model.g41406.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: -)Couldn't classify 417, 437
Sorry, prediction GeneMark_model.108507_t fails validation.
(GAG)	 AG	417-437	GT	AGG
(GAA)	 AG	464-478	GT	AGG
(GCT)	 AG	499-519	GT	GGG
(GAG)	 AG	540-615	GT	CTG
(CCA)	 AG	658-674	GT	GAG
(GGC)	 AG	713-727	GT	AGG
(GGA)	 AG	824-838	GT	GAG
(GGG)	 AG	887-908	GT	GGG
(GGA)	 AG	977-1084	TC	GAT
-recovered GeneMark_model.108507_t, terminal, 977, 1084
-recovered GeneMark_model.108507_t, internal, 417, 437
-recovered GeneMark_model.108507_t, internal, 464, 478
-recovered GeneMark_model.108507_t, internal, 499, 519
-recovered GeneMark_model.108507_t, internal, 540, 615
-recovered GeneMark_model.108507_t, internal, 658, 674
-recovered GeneMark_model.108507_t, internal, 713, 727
-recovered GeneMark_model.108507_t, internal, 824, 838
-recovered GeneMark_model.108507_t, internal, 887, 908

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

-building trellis in range 1 - 4188
-exon list size: 70


building trellis

1.4    
2.8    
4.2    
5.6    
6.9    
8.3    
9.7    
11.1    
12.5    
13.9    
15.3    
16.7    
18.1    
19.4    
20.8    
22.2    
23.6    
25.0    
26.4    
27.8    
29.2    
30.6    
31.9    
33.3    
34.7    
36.1    
37.5    
38.9    
40.3    
41.7    
43.1    
44.4    
45.8    
47.2    
48.6    
50.0    
51.4    
52.8    
54.2    
55.6    
56.9    
58.3    
59.7    
61.1    
62.5    
63.9    
65.3    
66.7    
68.1    
69.4    
70.8    
72.2    
73.6    
75.0    
76.4    
77.8    
79.2    
80.6    
81.9    
83.3    
84.7    
86.1    
87.5    
88.9    
90.3    
91.7    
93.1    
94.4    
95.8    
97.2    
98.6    
-found 1 predictions from path traversal

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