-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_621

-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_62059-T1
add_exon() Sorry, GlimmerHMM_glimmerT_62059-T1 1626-1935-terminal-1 is invalid.
Couldn't classify 1626, 1899
Sorry, prediction Augustus_model.g41251.t1 fails validation.
(ACC)	 AG	1626-1899	GT	AGG
(GAA)	 AG	2482-2514	GT	AGG
-recovered Augustus_model.g41251.t1, terminal, 2482, 2514
-recovered Augustus_model.g41251.t1, internal, 1626, 1899
-recovered Augustus_model.g41251.t1, internal, 2482, 2514
Couldn't classify 888, 908
Sorry, prediction GeneMark_model.108062_t fails validation.
(AGA)	 AG	888-908	GT	GAG
(AGT)	 AG	934-960	GT	GAG
(AGA)	 AG	984-1040	GT	GAG
(AGG)	 AG	1074-1109	GT	GAG
(AGG)	 AG	1143-1154	GT	GAG
(AGG)	 AG	1179-1205	GT	GAG
(GAC)	 AG	1232-1258	GT	GAG
(GAC)	 AG	1302-1358	GT	GAG
(GAC)	 AG	1397-1438	GT	GAG
(GAC)	 AG	1465-1491	GT	GAG
(AGA)	 AG	1523-1534	GT	GAG
(GAC)	 AG	1559-1570	GT	GAG
(ACC)	 AG	1626-1899	GT	AGG
(TAA)	 AG	2119-2121	GT	AAG
-recovered GeneMark_model.108062_t, terminal, 1559, 1570
-recovered GeneMark_model.108062_t, terminal, 2119, 2121
-recovered GeneMark_model.108062_t, internal, 888, 908
-recovered GeneMark_model.108062_t, internal, 934, 960
-recovered GeneMark_model.108062_t, internal, 984, 1040
-recovered GeneMark_model.108062_t, internal, 1074, 1109
-recovered GeneMark_model.108062_t, internal, 1143, 1154
-recovered GeneMark_model.108062_t, internal, 1179, 1205
-recovered GeneMark_model.108062_t, internal, 1232, 1258
-recovered GeneMark_model.108062_t, internal, 1302, 1358
-recovered GeneMark_model.108062_t, internal, 1397, 1438
-recovered GeneMark_model.108062_t, internal, 1465, 1491
-recovered GeneMark_model.108062_t, internal, 1523, 1534
-recovered GeneMark_model.108062_t, internal, 1559, 1570
-recovered GeneMark_model.108062_t, internal, 1626, 1899
-recovered GeneMark_model.108062_t, internal, 2119, 2121
Couldn't classify 808, 1205
Couldn't classify 4805, 4833
Sorry, prediction snap_scaffold_621-snap.1-T1 fails validation.
(TGT)	 AG	808-1205	GT	GAG
(ACC)	 AG	1626-1899	GT	AGG
(GTA)	 AG	2701-2752	GT	CAG
(GCA)	 AG	2894-2955	GT	AGG
(AGA)	 AG	4805-4833	GT	AAG
-recovered snap_scaffold_621-snap.1-T1, internal, 808, 1205
-recovered snap_scaffold_621-snap.1-T1, internal, 1626, 1899
-recovered snap_scaffold_621-snap.1-T1, internal, 2701, 2752
-recovered snap_scaffold_621-snap.1-T1, internal, 2894, 2955
-recovered snap_scaffold_621-snap.1-T1, internal, 4805, 4833

-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 592, 612
Sorry, prediction GeneMark_model.108063_t fails validation.
(AGA)	 AG	592-612	GT	GAG
(AGT)	 AG	640-654	GT	GAG
(GGA)	 AG	712-726	GT	GAG
(AGA)	 AG	754-774	GT	GAG
(AGA)	 AG	802-828	GT	CAG
(AGT)	 AG	860-868	GT	GAG
(GGA)	 AG	900-914	GT	GAG
(AAA)	 AG	940-954	GT	GAG
(GGA)	 AG	980-1001	AG	AGA
-recovered GeneMark_model.108063_t, terminal, 980, 1001
-recovered GeneMark_model.108063_t, internal, 592, 612
-recovered GeneMark_model.108063_t, internal, 640, 654
-recovered GeneMark_model.108063_t, internal, 712, 726
-recovered GeneMark_model.108063_t, internal, 754, 774
-recovered GeneMark_model.108063_t, internal, 802, 828
-recovered GeneMark_model.108063_t, internal, 860, 868
-recovered GeneMark_model.108063_t, internal, 900, 914
-recovered GeneMark_model.108063_t, internal, 940, 954

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

-building trellis in range 1 - 5361
-exon list size: 75


building trellis

1.3    
2.6    
3.9    
5.2    
6.5    
7.8    
9.1    
10.4    
11.7    
13.0    
14.3    
15.6    
16.9    
18.2    
19.5    
20.8    
22.1    
23.4    
24.7    
26.0    
27.3    
28.6    
29.9    
31.2    
32.5    
33.8    
35.1    
36.4    
37.7    
39.0    
40.3    
41.6    
42.9    
44.2    
45.5    
46.8    
48.1    
49.4    
50.6    
51.9    
53.2    
54.5    
55.8    
57.1    
58.4    
59.7    
61.0    
62.3    
63.6    
64.9    
66.2    
67.5    
68.8    
70.1    
71.4    
72.7    
74.0    
75.3    
76.6    
77.9    
79.2    
80.5    
81.8    
83.1    
84.4    
85.7    
87.0    
88.3    
89.6    
90.9    
92.2    
93.5    
94.8    
96.1    
97.4    
98.7    
-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