-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_294747-577461

-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 snap_scaffold_23-snap.74-T1
Valid prediction for snap_scaffold_23-snap.71-T1
Valid prediction for snap_scaffold_23-snap.59-T1
Valid prediction for GlimmerHMM_glimmerT_51545-T1
Valid prediction for GlimmerHMM_glimmerT_51567-T1
Valid prediction for Augustus_model.g34594.t1
Valid prediction for Augustus_model.g34613.t1
Valid prediction for snap_scaffold_23-snap.61-T1
Valid prediction for GeneMark_model.89717_t
Valid prediction for GlimmerHMM_glimmerT_51568-T1
Valid prediction for GlimmerHMM_glimmerT_51556-T1
Valid prediction for Augustus_model.g34606.t1
Valid prediction for Augustus_model.g34597.t1
Valid prediction for snap_scaffold_23-snap.40-T1
Valid prediction for snap_scaffold_23-snap.45-T1
Valid prediction for GeneMark_model.89701_t
Valid prediction for GeneMark_model.89688_t
Valid prediction for GlimmerHMM_glimmerT_51549-T1
Valid prediction for Augustus_model.g34585.t1
Valid prediction for GlimmerHMM_glimmerT_51552-T1
Valid prediction for Augustus_model.g34605.t1
Valid prediction for snap_scaffold_23-snap.73-T1
Valid prediction for GeneMark_model.89708_t
Valid prediction for Augustus_model.g34609.t1
Valid prediction for snap_scaffold_23-snap.63-T1
Valid prediction for Augustus_model.g34591.t1
Valid prediction for GeneMark_model.89702_t
Valid prediction for snap_scaffold_23-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_51542-T1
Valid prediction for snap_scaffold_23-snap.57-T1
Valid prediction for GlimmerHMM_glimmerT_51563-T1
Valid prediction for GlimmerHMM_glimmerT_51551-T1
Valid prediction for Augustus_model.g34596.t1
Valid prediction for GlimmerHMM_glimmerT_51559-T1
Valid prediction for snap_scaffold_23-snap.43-T1
Valid prediction for snap_scaffold_23-snap.78-T1
Couldn't classify 178339, 178366
Couldn't classify 178682, 178968
Sorry, prediction pasa_asmbl_31273.p1 fails validation.
(TGG)	 CC	178339-178366	GT	AGG
(GTG)	 AG	178682-178968	TA	GCT
Valid prediction for snap_scaffold_23-snap.79-T1
Valid prediction for GlimmerHMM_glimmerT_51560-T1
Valid prediction for GeneMark_model.89711_t
Valid prediction for snap_scaffold_23-snap.70-T1
Valid prediction for Augustus_model.g34598.t1
Valid prediction for GeneMark_model.89689_t
Valid prediction for snap_scaffold_23-snap.75-T1
Valid prediction for Augustus_model.g34595.t1
Valid prediction for GeneMark_model.89690_t
Valid prediction for Augustus_model.g34587.t1
Valid prediction for GlimmerHMM_glimmerT_51553-T1
Valid prediction for snap_scaffold_23-snap.44-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.41-T1
Valid prediction for Augustus_model.g34610.t1
Valid prediction for GlimmerHMM_glimmerT_51540-T1
Valid prediction for GeneMark_model.89707_t
Valid prediction for GeneMark_model.89716_t
Valid prediction for snap_scaffold_23-snap.68-T1
Valid prediction for snap_scaffold_23-snap.81-T1
Valid prediction for GlimmerHMM_glimmerT_51541-T1
Valid prediction for GlimmerHMM_glimmerT_51565-T1
Valid prediction for Augustus_model.g34611.t1
Valid prediction for snap_scaffold_23-snap.64-T1
Valid prediction for GlimmerHMM_glimmerT_51548-T1
Valid prediction for GlimmerHMM_glimmerT_51557-T1
Valid prediction for GeneMark_model.89704_t
Valid prediction for Augustus_model.g34614.t1
Valid prediction for Augustus_model.g34601.t1
Valid prediction for GlimmerHMM_glimmerT_51539-T1
Valid prediction for GeneMark_model.89718_t
Valid prediction for GeneMark_model.89719_t
Valid prediction for GlimmerHMM_glimmerT_51543-T1
Valid prediction for snap_scaffold_23-snap.76-T1
Valid prediction for snap_scaffold_23-snap.60-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.42-T1
Valid prediction for Augustus_model.g34586.t1
Valid prediction for Augustus_model.g34607.t1
Valid prediction for GeneMark_model.89694_t
Valid prediction for Augustus_model.g34600.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: -)Valid prediction for Augustus_model.g34588.t1
Valid prediction for GeneMark_model.89692_t
Valid prediction for snap_scaffold_23-snap.58-T1
Valid prediction for GeneMark_model.89693_t
Valid prediction for GlimmerHMM_glimmerT_51554-T1
Valid prediction for snap_scaffold_23-snap.56-T1
Valid prediction for GlimmerHMM_glimmerT_51561-T1
Valid prediction for GeneMark_model.89712_t
Valid prediction for GeneMark_model.89687_t
Valid prediction for HiQ_model.g34589.t1
Valid prediction for GeneMark_model.89695_t
Couldn't classify 252818, 252850
Couldn't classify 256391, 256523
Sorry, prediction pasa_asmbl_31301.p1 fails validation.
(CTC)	 AA	252818-252850	GT	AGG
(CTG)	 AG	252944-253040	GT	AGG
(ATC)	 AG	254096-254287	GT	GGG
(GAG)	 AG	254492-254592	GT	AGG
(GGC)	 AG	254764-254893	GT	TGG
(GGG)	 AG	254974-255103	GT	AGG
(GTG)	 AG	256090-256185	GT	AAG
(GGA)	 AG	256391-256523	CT	AAC
-recovered pasa_asmbl_31301.p1, internal, 252944, 253040
-recovered pasa_asmbl_31301.p1, internal, 254096, 254287
-recovered pasa_asmbl_31301.p1, internal, 254492, 254592
-recovered pasa_asmbl_31301.p1, internal, 254764, 254893
-recovered pasa_asmbl_31301.p1, internal, 254974, 255103
-recovered pasa_asmbl_31301.p1, internal, 256090, 256185
Valid prediction for Augustus_model.g34590.t1
Valid prediction for snap_scaffold_23-snap.55-T1
Valid prediction for GeneMark_model.89713_t
Valid prediction for GeneMark_model.89710_t
Valid prediction for GeneMark_model.89698_t
Valid prediction for GeneMark_model.89706_t
Valid prediction for pasa_asmbl_31316.p1
Valid prediction for GlimmerHMM_glimmerT_51544-T1
Valid prediction for snap_scaffold_23-snap.72-T1
Valid prediction for GeneMark_model.89715_t
Valid prediction for snap_scaffold_23-snap.51-T1
Valid prediction for snap_scaffold_23-snap.69-T1
Valid prediction for snap_scaffold_23-snap.52-T1
Valid prediction for pasa_asmbl_31312.p1
Valid prediction for GlimmerHMM_glimmerT_51538-T1
Valid prediction for snap_scaffold_23-snap.46-T1
Valid prediction for CodingQuarry_transcript_35469-T1
Valid prediction for GeneMark_model.89691_t
Valid prediction for GeneMark_model.89705_t
Valid prediction for GlimmerHMM_glimmerT_51546-T1
Valid prediction for Augustus_model.g34604.t1
Valid prediction for GlimmerHMM_glimmerT_51564-T1
Valid prediction for snap_scaffold_23-snap.54-T1
Valid prediction for HiQ_model.g34593.t1
Valid prediction for GlimmerHMM_glimmerT_51566-T1
Valid prediction for GlimmerHMM_glimmerT_51562-T1
Valid prediction for CodingQuarry_transcript_35468-T1
Valid prediction for Augustus_model.g34599.t1
Valid prediction for Augustus_model.g34584.t1
Valid prediction for GlimmerHMM_glimmerT_51547-T1
Valid prediction for GeneMark_model.89714_t
Couldn't classify 256688, 256788
Couldn't classify 263931, 264020
Sorry, prediction pasa_asmbl_31299.p1 fails validation.
(CAA)	 AG	256688-256788	GT	AGG
(ACA)	 AG	256878-257046	GT	AGG
(GCA)	 AG	259177-259227	GT	TGG
(CTG)	 AG	259349-259457	GT	AGG
(GTT)	 AG	259593-259729	GT	CGG
(GCT)	 AG	259852-259985	GT	AGG
(GAT)	 AG	260113-260195	GT	TGG
(GGA)	 AG	260311-260381	GT	AGG
(GCC)	 AG	260480-260604	GT	ACG
(TTT)	 AG	263563-263644	GT	CAG
(GAC)	 AG	263728-263811	GT	AGG
(AGT)	 AG	263931-264020	GT	AGG
-recovered pasa_asmbl_31299.p1, internal, 256688, 256788
-recovered pasa_asmbl_31299.p1, internal, 256878, 257046
-recovered pasa_asmbl_31299.p1, internal, 259177, 259227
-recovered pasa_asmbl_31299.p1, internal, 259349, 259457
-recovered pasa_asmbl_31299.p1, internal, 259593, 259729
-recovered pasa_asmbl_31299.p1, internal, 259852, 259985
-recovered pasa_asmbl_31299.p1, internal, 260113, 260195
-recovered pasa_asmbl_31299.p1, internal, 260311, 260381
-recovered pasa_asmbl_31299.p1, internal, 260480, 260604
-recovered pasa_asmbl_31299.p1, internal, 263563, 263644
-recovered pasa_asmbl_31299.p1, internal, 263728, 263811
-recovered pasa_asmbl_31299.p1, internal, 263931, 264020
Valid prediction for GlimmerHMM_glimmerT_51555-T1
Valid prediction for pasa_asmbl_31315.p1
Valid prediction for snap_scaffold_23-snap.49-T1
Valid prediction for snap_scaffold_23-snap.53-T1
Valid prediction for GeneMark_model.89696_t
Valid prediction for snap_scaffold_23-snap.66-T1
Valid prediction for Augustus_model.g34592.t1
Valid prediction for Augustus_model.g34602.t1
Valid prediction for GeneMark_model.89697_t
Couldn't classify 229511, 229831
Sorry, prediction pasa_asmbl_31306.p1 fails validation.
(AAT)	 AC	229511-229831	AC	GAA
Valid prediction for snap_scaffold_23-snap.62-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.77-T1
Valid prediction for Augustus_model.g34612.t1
Valid prediction for CodingQuarry_transcript_35467-T1
Valid prediction for CodingQuarry_transcript_35471-T1
Valid prediction for snap_scaffold_23-snap.50-T1
Couldn't classify 240167, 240397
Couldn't classify 241069, 241185
Sorry, prediction pasa_asmbl_31305.p1 fails validation.
(TGC)	 TC	240167-240397	GT	AAG
(GTC)	 AG	241069-241185	GT	AGG
-recovered pasa_asmbl_31305.p1, internal, 241069, 241185
Valid prediction for GeneMark_model.89709_t
Valid prediction for CodingQuarry_transcript_35473-T1
Valid prediction for GlimmerHMM_glimmerT_51550-T1
Valid prediction for GeneMark_model.89700_t
Valid prediction for snap_scaffold_23-snap.48-T1
Valid prediction for snap_scaffold_23-snap.39-T1
Valid prediction for Augustus_model.g34608.t1
Valid prediction for snap_scaffold_23-snap.47-T1
Valid prediction for Augustus_model.g34603.t1
Valid prediction for CodingQuarry_transcript_35470-T1
Valid prediction for snap_scaffold_23-snap.67-T1
Valid prediction for GlimmerHMM_glimmerT_51558-T1
Couldn't classify 267389, 267442
Couldn't classify 269050, 269177
Sorry, prediction pasa_asmbl_31298.p1 fails validation.
(ACA)	 CT	267389-267442	GT	GGG
(ACC)	 AG	268497-268589	GT	AGG
(GTG)	 AG	268710-268866	GT	AGG
(AGT)	 AG	269050-269177	GT	CAG
-recovered pasa_asmbl_31298.p1, internal, 268497, 268589
-recovered pasa_asmbl_31298.p1, internal, 268710, 268866
-recovered pasa_asmbl_31298.p1, internal, 269050, 269177
Valid prediction for GeneMark_model.89720_t
Valid prediction for CodingQuarry_transcript_35472-T1
Valid prediction for snap_scaffold_23-snap.65-T1

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

-building trellis in range 1 - 282715
-exon list size: 481


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 37 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 35 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 257863 - 282715
-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 257863 - 268757
-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

-building DP trellis

-building trellis in range 258203 - 268757
-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

-building DP trellis

-building trellis in range 268801 - 282715
-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