-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_3926401-4190887

-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.g373.t1
Valid prediction for snap_scaffold_1-snap.620-T1
Valid prediction for GlimmerHMM_glimmerT_482-T1
Valid prediction for snap_scaffold_1-snap.606-T1
Couldn't classify 168113, 168469
Sorry, prediction pasa_asmbl_1630.p1 fails validation.
(CAA)	 GT	168113-168469	GC	GAG
Valid prediction for snap_scaffold_1-snap.604-T1
Valid prediction for snap_scaffold_1-snap.597-T1
Valid prediction for GlimmerHMM_glimmerT_470-T1
Valid prediction for snap_scaffold_1-snap.599-T1
Valid prediction for GeneMark_model.568_t
Valid prediction for snap_scaffold_1-snap.611-T1
Valid prediction for snap_scaffold_1-snap.612-T1
Valid prediction for snap_scaffold_1-snap.593-T1
Valid prediction for snap_scaffold_1-snap.619-T1
Valid prediction for GlimmerHMM_glimmerT_465-T1
Valid prediction for snap_scaffold_1-snap.594-T1
Valid prediction for snap_scaffold_1-snap.610-T1
Valid prediction for snap_scaffold_1-snap.615-T1
Valid prediction for snap_scaffold_1-snap.613-T1
Valid prediction for Augustus_model.g383.t1
Valid prediction for GeneMark_model.558_t
Valid prediction for GeneMark_model.543_t
Valid prediction for GeneMark_model.542_t
Valid prediction for Augustus_model.g381.t1
Valid prediction for Augustus_model.g386.t1
Valid prediction for GeneMark_model.556_t
Valid prediction for GlimmerHMM_glimmerT_477-T1
Valid prediction for snap_scaffold_1-snap.614-T1
Valid prediction for GlimmerHMM_glimmerT_484-T1
Valid prediction for GeneMark_model.547_t
Valid prediction for GeneMark_model.562_t
Valid prediction for GeneMark_model.540_t
Valid prediction for GlimmerHMM_glimmerT_487-T1
Valid prediction for snap_scaffold_1-snap.595-T1
Valid prediction for GeneMark_model.536_t
Valid prediction for Augustus_model.g372.t1
Valid prediction for GeneMark_model.553_t
Valid prediction for snap_scaffold_1-snap.605-T1
Valid prediction for GeneMark_model.545_t
Valid prediction for Augustus_model.g378.t1
Valid prediction for GlimmerHMM_glimmerT_471-T1
Couldn't classify 192275, 192536
Sorry, prediction pasa_asmbl_1635.p1 fails validation.
(AAA)	 AT	192275-192536	GT	AGG
(GGG)	 AG	192882-193000	GT	AGG
(TTT)	 AG	193611-193739	GT	TGG
(GTG)	 AG	194504-194681	GT	AGG
(TTT)	 AG	194958-195093	GT	TGG
(GAA)	 AG	195303-195406	GT	AGG
(GAG)	 AG	195504-195743	GT	AGG
(GAT)	 AG	195881-196156	GT	AGG
(AGA)	 AG	196592-196752	GT	GAG
(ATT)	 AG	198482-198618	GT	AGG
(ACT)	 AG	199396-199546	GC	AGG
-recovered pasa_asmbl_1635.p1, terminal, 199396, 199546
-recovered pasa_asmbl_1635.p1, internal, 192882, 193000
-recovered pasa_asmbl_1635.p1, internal, 193611, 193739
-recovered pasa_asmbl_1635.p1, internal, 194504, 194681
-recovered pasa_asmbl_1635.p1, internal, 194958, 195093
-recovered pasa_asmbl_1635.p1, internal, 195303, 195406
-recovered pasa_asmbl_1635.p1, internal, 195504, 195743
-recovered pasa_asmbl_1635.p1, internal, 195881, 196156
-recovered pasa_asmbl_1635.p1, internal, 196592, 196752
-recovered pasa_asmbl_1635.p1, internal, 198482, 198618
-recovered pasa_asmbl_1635.p1, internal, 199396, 199546
Valid prediction for GlimmerHMM_glimmerT_486-T1
Valid prediction for Augustus_model.g371.t1
Couldn't classify 171809, 171859
Couldn't classify 176826, 176871
Sorry, prediction pasa_asmbl_1632.p1 fails validation.
(AGA)	 CC	171809-171859	GT	AGG
(GAG)	 AG	172564-172650	GT	AGG
(ATG)	 AG	173055-173171	GT	AGG
(AAA)	 AG	176107-176205	GT	ACG
(GAT)	 AG	176318-176466	GT	AGG
(GGA)	 AG	176826-176871	AG	AGA
-recovered pasa_asmbl_1632.p1, initial, 173055, 173171
-recovered pasa_asmbl_1632.p1, terminal, 176318, 176466
-recovered pasa_asmbl_1632.p1, internal, 172564, 172650
-recovered pasa_asmbl_1632.p1, internal, 173055, 173171
-recovered pasa_asmbl_1632.p1, internal, 176107, 176205
-recovered pasa_asmbl_1632.p1, internal, 176318, 176466
Valid prediction for Augustus_model.g377.t1
Valid prediction for HiQ_model.g384.t1
Valid prediction for GlimmerHMM_glimmerT_476-T1
Valid prediction for GeneMark_model.538_t
Valid prediction for GeneMark_model.559_t
Valid prediction for snap_scaffold_1-snap.616-T1
Valid prediction for snap_scaffold_1-snap.601-T1
Valid prediction for snap_scaffold_1-snap.607-T1
Couldn't classify 168623, 168800
Couldn't classify 170215, 170390
Sorry, prediction pasa_asmbl_1631.p1 fails validation.
(CTG)	 CG	168623-168800	GT	AGG
(ACT)	 AG	170215-170390	CT	ACC
Valid prediction for GeneMark_model.565_t
Valid prediction for snap_scaffold_1-snap.608-T1
Valid prediction for GlimmerHMM_glimmerT_483-T1
Valid prediction for snap_scaffold_1-snap.617-T1
Valid prediction for pasa_asmbl_1633.p1
Valid prediction for GeneMark_model.563_t
Valid prediction for GlimmerHMM_glimmerT_479-T1
Valid prediction for GeneMark_model.555_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: -)Valid prediction for Augustus_model.g375.t1
Valid prediction for GlimmerHMM_glimmerT_467-T1
Valid prediction for GlimmerHMM_glimmerT_478-T1
Valid prediction for snap_scaffold_1-snap.618-T1
Valid prediction for GeneMark_model.551_t
Valid prediction for snap_scaffold_1-snap.609-T1
Valid prediction for GlimmerHMM_glimmerT_490-T1
Valid prediction for GlimmerHMM_glimmerT_474-T1
Valid prediction for CodingQuarry_transcript_2577-T1
Valid prediction for GeneMark_model.557_t
Valid prediction for GeneMark_model.541_t
Valid prediction for GlimmerHMM_glimmerT_468-T1
Valid prediction for GlimmerHMM_glimmerT_475-T1
Valid prediction for GeneMark_model.546_t
Valid prediction for snap_scaffold_1-snap.603-T1
Valid prediction for GeneMark_model.539_t
Valid prediction for GlimmerHMM_glimmerT_485-T1
Valid prediction for GlimmerHMM_glimmerT_488-T1
Valid prediction for GeneMark_model.550_t
Valid prediction for snap_scaffold_1-snap.598-T1
Couldn't classify 158482, 158530
Sorry, prediction pasa_asmbl_179.p1 fails validation.
(GAA)	 AC	158482-158530	GT	AGG
(AGA)	 AG	159874-159970	GT	CGG
(GTT)	 AG	161194-161274	GT	AGG
(CGA)	 AG	163057-163111	GT	AGG
(CAA)	 AG	164360-164518	CC	AGC
-recovered pasa_asmbl_179.p1, terminal, 164360, 164518
-recovered pasa_asmbl_179.p1, internal, 159874, 159970
-recovered pasa_asmbl_179.p1, internal, 161194, 161274
-recovered pasa_asmbl_179.p1, internal, 163057, 163111
Valid prediction for snap_scaffold_1-snap.602-T1
Valid prediction for GeneMark_model.548_t
Valid prediction for GeneMark_model.567_t
Valid prediction for GeneMark_model.564_t
Valid prediction for pasa_asmbl_177.p1
Valid prediction for GeneMark_model.537_t
Valid prediction for GlimmerHMM_glimmerT_481-T1
Valid prediction for Augustus_model.g382.t1
Valid prediction for GlimmerHMM_glimmerT_472-T1
Valid prediction for GlimmerHMM_glimmerT_473-T1
Valid prediction for GeneMark_model.549_t
Valid prediction for snap_scaffold_1-snap.600-T1
Valid prediction for GeneMark_model.552_t
Valid prediction for GeneMark_model.554_t
Valid prediction for GlimmerHMM_glimmerT_466-T1
Valid prediction for Augustus_model.g380.t1
Valid prediction for Augustus_model.g379.t1
Valid prediction for CodingQuarry_transcript_2579-T1
Valid prediction for Augustus_model.g385.t1
Valid prediction for Augustus_model.g376.t1
Valid prediction for GeneMark_model.544_t
Valid prediction for GlimmerHMM_glimmerT_480-T1
Valid prediction for GlimmerHMM_glimmerT_469-T1
Valid prediction for CodingQuarry_transcript_2578-T1
Valid prediction for GeneMark_model.566_t
Valid prediction for HiQ_model.g374.t1
Valid prediction for GlimmerHMM_glimmerT_489-T1
Valid prediction for snap_scaffold_1-snap.596-T1
Valid prediction for GeneMark_model.561_t

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

-building trellis in range 1 - 264487
-exon list size: 368


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.1    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.8    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.5    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
13.8    
14.1    
14.3    
14.6    
14.9    
15.1    
15.4    
15.7    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.4    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.4    
28.6    
28.9    
29.2    
29.5    
29.7    
30.0    
30.3    
30.5    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.5    
69.7    
70.0    
70.3    
70.5    
70.8    
71.1    
71.4    
71.6    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.3    
84.6    
84.9    
85.1    
85.4    
85.7    
85.9    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 20 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 212927 - 264487
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-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 212927 - 229680
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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 212927 - 229578
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 212927 - 227129
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 215060 - 227129
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 229690 - 264487
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-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 235976 - 264487
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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 235976 - 261475
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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 236075 - 261475
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 236075 - 256302
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 236075 - 250282
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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