-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_700

-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 Augustus_model.g41302.t1
Couldn't classify 3205, 3301
Sorry, prediction snap_scaffold_700-snap.2-T1 fails validation.
(ATG)	 GC	1357-1404	GT	AGG
(CGA)	 AG	2968-3088	GT	GGG
(GAT)	 AG	3205-3301	GT	AGG
-recovered snap_scaffold_700-snap.2-T1, initial, 1357, 1404
-recovered snap_scaffold_700-snap.2-T1, internal, 2968, 3088
-recovered snap_scaffold_700-snap.2-T1, internal, 3205, 3301
Valid prediction for GlimmerHMM_glimmerT_62135-T1
Valid prediction for GeneMark_model.108224_t
Valid prediction for snap_scaffold_700-snap.1-T1
add_exon() Sorry, snap_scaffold_700-snap.1-T1 777-973-terminal-1 is invalid.
Couldn't classify 590, 601
Sorry, prediction GeneMark_model.108223_t fails validation.
(GGT)	 AG	590-601	GT	AGG
(AGA)	 AG	666-707	GT	GGG
(AGG)	 AG	730-846	GT	CAG
(AGA)	 AG	868-948	GT	GAG
(GGA)	 AG	979-993	GT	GAG
(AGA)	 AG	1015-1092	GT	GAG
(AGA)	 AG	1138-1254	GT	GAG
(GAT)	 AG	1331-1351	GT	ACG
(GAT)	 AG	1381-1404	GT	AGG
(GGA)	 AG	1438-1446	GC	GAG
(AGA)	 AG	1480-1542	GT	GAG
(TGA)	 AG	1572-1598	GT	GAG
(AGA)	 AG	1620-1628	GC	GGG
(GCT)	 AG	1654-1743	GT	AGG
(ATG)	 AG	1769-1910	GC	GAG
add_exon() Sorry, GeneMark_model.108223_t 1769-1910-initial-1 is invalid.
-recovered GeneMark_model.108223_t, initial, 1769, 1910
-recovered GeneMark_model.108223_t, terminal, 979, 993
-recovered GeneMark_model.108223_t, terminal, 1769, 1910
-recovered GeneMark_model.108223_t, internal, 590, 601
-recovered GeneMark_model.108223_t, internal, 666, 707
-recovered GeneMark_model.108223_t, internal, 730, 846
-recovered GeneMark_model.108223_t, internal, 868, 948
-recovered GeneMark_model.108223_t, internal, 979, 993
-recovered GeneMark_model.108223_t, internal, 1015, 1092
-recovered GeneMark_model.108223_t, internal, 1138, 1254
-recovered GeneMark_model.108223_t, internal, 1331, 1351
-recovered GeneMark_model.108223_t, internal, 1381, 1404
-recovered GeneMark_model.108223_t, internal, 1438, 1446
-recovered GeneMark_model.108223_t, internal, 1480, 1542
-recovered GeneMark_model.108223_t, internal, 1572, 1598
-recovered GeneMark_model.108223_t, internal, 1620, 1628
-recovered GeneMark_model.108223_t, internal, 1654, 1743
-recovered GeneMark_model.108223_t, internal, 1769, 1910

-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 328, 389
Sorry, prediction GlimmerHMM_glimmerT_62136-T1 fails validation.
(CAA)	 AG	328-389	GT	AAG
(GCG)	 AG	578-662	GT	AGG
(GCG)	 AG	1259-1368	TC	GAT
add_exon() Sorry, GlimmerHMM_glimmerT_62136-T1 578-662-terminal-3 is invalid.
-recovered GlimmerHMM_glimmerT_62136-T1, terminal, 578, 662
-recovered GlimmerHMM_glimmerT_62136-T1, terminal, 1259, 1368
-recovered GlimmerHMM_glimmerT_62136-T1, internal, 328, 389
-recovered GlimmerHMM_glimmerT_62136-T1, internal, 578, 662
Couldn't classify 328, 391
Sorry, prediction GeneMark_model.108225_t fails validation.
(CAA)	 AG	328-391	GT	GTG
(CAG)	 AG	491-540	GT	CAG
(GCG)	 AG	578-587	GT	ATG
(AGC)	 AG	1039-1133	GT	AGG
(GCG)	 AG	1259-1368	TC	GAT
-recovered GeneMark_model.108225_t, terminal, 1259, 1368
-recovered GeneMark_model.108225_t, internal, 328, 391
-recovered GeneMark_model.108225_t, internal, 491, 540
-recovered GeneMark_model.108225_t, internal, 578, 587
-recovered GeneMark_model.108225_t, internal, 1039, 1133

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

-building trellis in range 1 - 4935
-exon list size: 52


building trellis

1.9    
3.7    
5.6    
7.4    
9.3    
11.1    
13.0    
14.8    
16.7    
18.5    
20.4    
22.2    
24.1    
25.9    
27.8    
29.6    
31.5    
33.3    
35.2    
37.0    
38.9    
40.7    
42.6    
44.4    
46.3    
48.1    
50.0    
51.9    
53.7    
55.6    
57.4    
59.3    
61.1    
63.0    
64.8    
66.7    
68.5    
70.4    
72.2    
74.1    
75.9    
77.8    
79.6    
81.5    
83.3    
85.2    
87.0    
88.9    
90.7    
92.6    
94.4    
96.3    
98.1    
-found 3 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

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