-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_10912168-11215799

-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_4612-T1
Valid prediction for GlimmerHMM_glimmerT_4617-T1
Valid prediction for snap_scaffold_2-snap.2181-T1
Valid prediction for GeneMark_model.7367_t
Valid prediction for GlimmerHMM_glimmerT_4602-T1
Valid prediction for snap_scaffold_2-snap.2188-T1
Valid prediction for GeneMark_model.7379_t
Valid prediction for snap_scaffold_2-snap.2193-T1
Valid prediction for snap_scaffold_2-snap.2191-T1
Valid prediction for snap_scaffold_2-snap.2190-T1
Valid prediction for GeneMark_model.7376_t
Valid prediction for GeneMark_model.7374_t
Valid prediction for snap_scaffold_2-snap.2192-T1
Valid prediction for snap_scaffold_2-snap.2180-T1
Valid prediction for GlimmerHMM_glimmerT_4610-T1
Valid prediction for Augustus_model.g3095.t1
Valid prediction for GeneMark_model.7378_t
Valid prediction for GeneMark_model.7388_t
Valid prediction for GlimmerHMM_glimmerT_4616-T1
Valid prediction for GeneMark_model.7365_t
Valid prediction for GlimmerHMM_glimmerT_4611-T1
Valid prediction for GlimmerHMM_glimmerT_4604-T1
Valid prediction for GlimmerHMM_glimmerT_4609-T1
Valid prediction for GeneMark_model.7384_t
Valid prediction for GlimmerHMM_glimmerT_4619-T1
Valid prediction for Augustus_model.g3093.t1
Valid prediction for snap_scaffold_2-snap.2184-T1
Valid prediction for GeneMark_model.7368_t
Valid prediction for GeneMark_model.7387_t
Valid prediction for GlimmerHMM_glimmerT_4614-T1
Valid prediction for GeneMark_model.7391_t

-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 33141, 33723
Couldn't classify 34356, 34416
Sorry, prediction pasa_asmbl_23459.p1 fails validation.
(GTC)	 GA	33141-33723	GT	AGG
(GCT)	 AG	33858-33984	GT	AGG
(CAC)	 AG	34356-34416	GA	TGG
-recovered pasa_asmbl_23459.p1, internal, 33858, 33984
Valid prediction for GeneMark_model.7386_t
Valid prediction for Augustus_model.g3096.t1
Valid prediction for GlimmerHMM_glimmerT_4603-T1
Valid prediction for GlimmerHMM_glimmerT_4613-T1
Valid prediction for snap_scaffold_2-snap.2189-T1
Valid prediction for GeneMark_model.7377_t
Valid prediction for HiQ_model.g3097.t1
Valid prediction for GeneMark_model.7385_t
Valid prediction for GlimmerHMM_glimmerT_4606-T1
Valid prediction for GeneMark_model.7366_t
Valid prediction for GeneMark_model.7383_t
Valid prediction for GeneMark_model.7389_t
Valid prediction for GeneMark_model.7382_t
Valid prediction for GeneMark_model.7392_t
Valid prediction for snap_scaffold_2-snap.2187-T1
Valid prediction for GlimmerHMM_glimmerT_4608-T1
Valid prediction for GlimmerHMM_glimmerT_4618-T1
Valid prediction for GeneMark_model.7370_t
Valid prediction for snap_scaffold_2-snap.2195-T1
Valid prediction for GeneMark_model.7373_t
Valid prediction for GeneMark_model.7380_t
Valid prediction for snap_scaffold_2-snap.2182-T1
Valid prediction for snap_scaffold_2-snap.2183-T1
Valid prediction for GeneMark_model.7369_t
Valid prediction for GlimmerHMM_glimmerT_4607-T1
Valid prediction for snap_scaffold_2-snap.2194-T1
Couldn't classify 36060, 36208
Sorry, prediction pasa_asmbl_23458.p1 fails validation.
(GAC)	 TA	36060-36208	GT	TGG
(GCA)	 AG	36409-36628	GA	AGG
-recovered pasa_asmbl_23458.p1, terminal, 36409, 36628
Valid prediction for GlimmerHMM_glimmerT_4605-T1
Valid prediction for snap_scaffold_2-snap.2185-T1
Valid prediction for Augustus_model.g3094.t1
Valid prediction for GeneMark_model.7381_t
Valid prediction for GeneMark_model.7390_t
Valid prediction for snap_scaffold_2-snap.2186-T1
Valid prediction for GeneMark_model.7372_t
Valid prediction for GlimmerHMM_glimmerT_4615-T1
Valid prediction for GeneMark_model.7375_t
Valid prediction for snap_scaffold_2-snap.2179-T1
Valid prediction for CodingQuarry_transcript_28620-T1
Valid prediction for GeneMark_model.7371_t
Valid prediction for GlimmerHMM_glimmerT_4620-T1
Valid prediction for pasa_asmbl_23462.p1

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

-building trellis in range 1 - 303632
-exon list size: 257


building trellis

0.4    
0.8    
1.2    
1.5    
1.9    
2.3    
2.7    
3.1    
3.5    
3.9    
4.2    
4.6    
5.0    
5.4    
5.8    
6.2    
6.6    
6.9    
7.3    
7.7    
8.1    
8.5    
8.9    
9.3    
9.7    
10.0    
10.4    
10.8    
11.2    
11.6    
12.0    
12.4    
12.7    
13.1    
13.5    
13.9    
14.3    
14.7    
15.1    
15.4    
15.8    
16.2    
16.6    
17.0    
17.4    
17.8    
18.1    
18.5    
18.9    
19.3    
19.7    
20.1    
20.5    
20.8    
21.2    
21.6    
22.0    
22.4    
22.8    
23.2    
23.6    
23.9    
24.3    
24.7    
25.1    
25.5    
25.9    
26.3    
26.6    
27.0    
27.4    
27.8    
28.2    
28.6    
29.0    
29.3    
29.7    
30.1    
30.5    
30.9    
31.3    
31.7    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.7    
35.1    
35.5    
35.9    
36.3    
36.7    
37.1    
37.5    
37.8    
38.2    
38.6    
39.0    
39.4    
39.8    
40.2    
40.5    
40.9    
41.3    
41.7    
42.1    
42.5    
42.9    
43.2    
43.6    
44.0    
44.4    
44.8    
45.2    
45.6    
45.9    
46.3    
46.7    
47.1    
47.5    
47.9    
48.3    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.7    
52.1    
52.5    
52.9    
53.3    
53.7    
54.1    
54.4    
54.8    
55.2    
55.6    
56.0    
56.4    
56.8    
57.1    
57.5    
57.9    
58.3    
58.7    
59.1    
59.5    
59.8    
60.2    
60.6    
61.0    
61.4    
61.8    
62.2    
62.5    
62.9    
63.3    
63.7    
64.1    
64.5    
64.9    
65.3    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.3    
68.7    
69.1    
69.5    
69.9    
70.3    
70.7    
71.0    
71.4    
71.8    
72.2    
72.6    
73.0    
73.4    
73.7    
74.1    
74.5    
74.9    
75.3    
75.7    
76.1    
76.4    
76.8    
77.2    
77.6    
78.0    
78.4    
78.8    
79.2    
79.5    
79.9    
80.3    
80.7    
81.1    
81.5    
81.9    
82.2    
82.6    
83.0    
83.4    
83.8    
84.2    
84.6    
84.9    
85.3    
85.7    
86.1    
86.5    
86.9    
87.3    
87.6    
88.0    
88.4    
88.8    
89.2    
89.6    
90.0    
90.3    
90.7    
91.1    
91.5    
91.9    
92.3    
92.7    
93.1    
93.4    
93.8    
94.2    
94.6    
95.0    
95.4    
95.8    
96.1    
96.5    
96.9    
97.3    
97.7    
98.1    
98.5    
98.8    
99.2    
99.6    
-found 13 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 5 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10146
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 289438 - 303632
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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

-building DP trellis

-building trellis in range 289438 - 300451
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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