-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_19192765-19369362

-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 GeneMark_model.23629_t
Valid prediction for GeneMark_model.23610_t
Valid prediction for snap_scaffold_5-snap.3653-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3614-T1
Valid prediction for GlimmerHMM_glimmerT_14111-T1
Valid prediction for snap_scaffold_5-snap.3627-T1
Valid prediction for GeneMark_model.23608_t
Valid prediction for Augustus_model.g9421.t1
Valid prediction for Augustus_model.g9419.t1
Valid prediction for GeneMark_model.23625_t
Valid prediction for snap_scaffold_5-snap.3622-T1
Valid prediction for GlimmerHMM_glimmerT_14126-T1
Valid prediction for GeneMark_model.23612_t
Valid prediction for Augustus_model.g9424.t1
Valid prediction for Augustus_model.g9418.t1
Valid prediction for GeneMark_model.23605_t
Valid prediction for snap_scaffold_5-snap.3630-T1
Valid prediction for GeneMark_model.23616_t
Valid prediction for Augustus_model.g9417.t1
Valid prediction for GlimmerHMM_glimmerT_14113-T1
Valid prediction for snap_scaffold_5-snap.3624-T1
Valid prediction for GlimmerHMM_glimmerT_14135-T1
Valid prediction for GlimmerHMM_glimmerT_14106-T1
Valid prediction for GlimmerHMM_glimmerT_14114-T1
Valid prediction for GlimmerHMM_glimmerT_14107-T1
Valid prediction for GlimmerHMM_glimmerT_14102-T1
Valid prediction for GlimmerHMM_glimmerT_14119-T1
Valid prediction for GeneMark_model.23620_t
Valid prediction for GeneMark_model.23630_t
Valid prediction for Augustus_model.g9426.t1
Valid prediction for snap_scaffold_5-snap.3615-T1
Valid prediction for GeneMark_model.23606_t
Valid prediction for GeneMark_model.23623_t
Valid prediction for GlimmerHMM_glimmerT_14105-T1
Valid prediction for snap_scaffold_5-snap.3620-T1
Valid prediction for GeneMark_model.23618_t
Valid prediction for Augustus_model.g9425.t1
Valid prediction for GlimmerHMM_glimmerT_14097-T1
Valid prediction for snap_scaffold_5-snap.3623-T1
Valid prediction for GeneMark_model.23619_t
Valid prediction for Augustus_model.g9451.t1
Valid prediction for snap_scaffold_5-snap.3654-T1
Couldn't classify 86352, 86479
Sorry, prediction pasa_asmbl_44964.p1 fails validation.
(ATG)	 AT	81348-81435	GT	TCG
(AGG)	 AG	83980-84108	GT	AGG
(GAA)	 AG	84208-84313	GT	ATG
(TGA)	 AG	84459-84528	GT	AGG
(GAG)	 AG	85013-85105	GT	AGG
(AAT)	 AG	85247-85310	GT	GGG
(GGA)	 AG	85437-85515	GT	AGG
(GAA)	 AG	85613-85691	GT	AGG
(GCC)	 AG	85899-86032	GT	AGG
(GGC)	 AG	86146-86240	GT	AGG
(GTG)	 AG	86352-86479	GT	AGG
-recovered pasa_asmbl_44964.p1, initial, 81348, 81435
-recovered pasa_asmbl_44964.p1, internal, 83980, 84108
-recovered pasa_asmbl_44964.p1, internal, 84208, 84313
-recovered pasa_asmbl_44964.p1, internal, 84459, 84528
-recovered pasa_asmbl_44964.p1, internal, 85013, 85105
-recovered pasa_asmbl_44964.p1, internal, 85247, 85310
-recovered pasa_asmbl_44964.p1, internal, 85437, 85515
-recovered pasa_asmbl_44964.p1, internal, 85613, 85691
-recovered pasa_asmbl_44964.p1, internal, 85899, 86032
-recovered pasa_asmbl_44964.p1, internal, 86146, 86240
-recovered pasa_asmbl_44964.p1, internal, 86352, 86479
Valid prediction for snap_scaffold_5-snap.3638-T1
Valid prediction for Augustus_model.g9437.t1
Valid prediction for GeneMark_model.23611_t
Valid prediction for HiQ_model.g9430.t1
Valid prediction for GlimmerHMM_glimmerT_14120-T1
Valid prediction for Augustus_model.g9432.t1
Valid prediction for GlimmerHMM_glimmerT_14129-T1
Valid prediction for GlimmerHMM_glimmerT_14099-T1
Valid prediction for Augustus_model.g9429.t1
Valid prediction for GlimmerHMM_glimmerT_14103-T1
Valid prediction for snap_scaffold_5-snap.3644-T1
Valid prediction for Augustus_model.g9442.t1
Valid prediction for snap_scaffold_5-snap.3618-T1
Valid prediction for Augustus_model.g9441.t1
Valid prediction for GlimmerHMM_glimmerT_14134-T1
Valid prediction for GlimmerHMM_glimmerT_14098-T1
Valid prediction for snap_scaffold_5-snap.3626-T1
Valid prediction for GlimmerHMM_glimmerT_14124-T1
Valid prediction for Augustus_model.g9436.t1
Valid prediction for Augustus_model.g9427.t1
Valid prediction for GlimmerHMM_glimmerT_14104-T1
Valid prediction for GeneMark_model.23614_t
Valid prediction for Augustus_model.g9435.t1
Valid prediction for GeneMark_model.23615_t
Valid prediction for CodingQuarry_transcript_52354-T1
Valid prediction for snap_scaffold_5-snap.3621-T1
Valid prediction for GlimmerHMM_glimmerT_14109-T1
Valid prediction for GlimmerHMM_glimmerT_14115-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g9431.t1
Valid prediction for Augustus_model.g9450.t1
Valid prediction for GlimmerHMM_glimmerT_14121-T1
Valid prediction for snap_scaffold_5-snap.3640-T1
Couldn't classify 18831, 19247
Sorry, prediction pasa_asmbl_46408.p1 fails validation.
(GGG)	 TG	18831-19247	TC	ACT
Valid prediction for snap_scaffold_5-snap.3639-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 GeneMark_model.23617_t
Valid prediction for GlimmerHMM_glimmerT_14131-T1
Valid prediction for snap_scaffold_5-snap.3655-T1
Valid prediction for GlimmerHMM_glimmerT_14108-T1
Valid prediction for GlimmerHMM_glimmerT_14128-T1
Valid prediction for snap_scaffold_5-snap.3631-T1
Valid prediction for snap_scaffold_5-snap.3643-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3629-T1
Valid prediction for Augustus_model.g9438.t1
Valid prediction for GeneMark_model.23609_t
Valid prediction for snap_scaffold_5-snap.3634-T1
Valid prediction for Augustus_model.g9447.t1
Valid prediction for GlimmerHMM_glimmerT_14130-T1
Valid prediction for snap_scaffold_5-snap.3635-T1
Valid prediction for snap_scaffold_5-snap.3632-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3628-T1
Valid prediction for Augustus_model.g9440.t1
Valid prediction for GlimmerHMM_glimmerT_14123-T1
Valid prediction for snap_scaffold_5-snap.3636-T1
Valid prediction for Augustus_model.g9433.t1
Valid prediction for Augustus_model.g9449.t1
Valid prediction for GeneMark_model.23622_t
Valid prediction for snap_scaffold_5-snap.3645-T1
Valid prediction for GlimmerHMM_glimmerT_14112-T1
Valid prediction for Augustus_model.g9422.t1
Valid prediction for GlimmerHMM_glimmerT_14122-T1
Valid prediction for GlimmerHMM_glimmerT_14125-T1
Valid prediction for GlimmerHMM_glimmerT_14100-T1
Valid prediction for GlimmerHMM_glimmerT_14132-T1
Valid prediction for GlimmerHMM_glimmerT_14096-T1
Valid prediction for Augustus_model.g9428.t1
Valid prediction for snap_scaffold_5-snap.3619-T1
Valid prediction for GeneMark_model.23626_t
Valid prediction for GlimmerHMM_glimmerT_14117-T1
Valid prediction for snap_scaffold_5-snap.3633-T1
Valid prediction for GlimmerHMM_glimmerT_14116-T1
Valid prediction for GlimmerHMM_glimmerT_14127-T1
Valid prediction for GlimmerHMM_glimmerT_14101-T1
Valid prediction for Augustus_model.g9439.t1
Valid prediction for Augustus_model.g9445.t1
Valid prediction for snap_scaffold_5-snap.3641-T1
Valid prediction for snap_scaffold_5-snap.3617-T1
Valid prediction for GeneMark_model.23627_t
Valid prediction for GlimmerHMM_glimmerT_14133-T1
Valid prediction for HiQ_model.g9443.t1
Valid prediction for snap_scaffold_5-snap.3646-T1
Valid prediction for snap_scaffold_5-snap.3647-T1
Valid prediction for GeneMark_model.23628_t
Valid prediction for HiQ_model.g9420.t1
Valid prediction for snap_scaffold_5-snap.3652-T1
Valid prediction for GlimmerHMM_glimmerT_14110-T1
Valid prediction for Augustus_model.g9448.t1
Valid prediction for snap_scaffold_5-snap.3650-T1
Valid prediction for Augustus_model.g9446.t1
Valid prediction for GeneMark_model.23607_t
Valid prediction for GlimmerHMM_glimmerT_14118-T1
Valid prediction for snap_scaffold_5-snap.3616-T1
Valid prediction for Augustus_model.g9434.t1
Valid prediction for HiQ_model.g9444.t1
Valid prediction for snap_scaffold_5-snap.3637-T1
Valid prediction for snap_scaffold_5-snap.3649-T1
Valid prediction for Augustus_model.g9423.t1
Valid prediction for pasa_asmbl_46274.p1
Valid prediction for snap_scaffold_5-snap.3625-T1
Valid prediction for GeneMark_model.23613_t
Valid prediction for CodingQuarry_transcript_52355-T1
Valid prediction for snap_scaffold_5-snap.3648-T1
Valid prediction for GeneMark_model.23624_t
Valid prediction for snap_scaffold_5-snap.3651-T1
Valid prediction for snap_scaffold_5-snap.3642-T1

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

-building trellis in range 1 - 176598
-exon list size: 428


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
2.1    
2.3    
2.6    
2.8    
3.0    
3.3    
3.5    
3.7    
4.0    
4.2    
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4.7    
4.9    
5.1    
5.3    
5.6    
5.8    
6.0    
6.3    
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6.7    
7.0    
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7.9    
8.1    
8.4    
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8.8    
9.1    
9.3    
9.5    
9.8    
10.0    
10.2    
10.5    
10.7    
10.9    
11.2    
11.4    
11.6    
11.9    
12.1    
12.3    
12.6    
12.8    
13.0    
13.3    
13.5    
13.7    
14.0    
14.2    
14.4    
14.7    
14.9    
15.1    
15.3    
15.6    
15.8    
16.0    
16.3    
16.5    
16.7    
17.0    
17.2    
17.4    
17.7    
17.9    
18.1    
18.4    
18.6    
18.8    
19.1    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
20.9    
21.2    
21.4    
21.6    
21.9    
22.1    
22.3    
22.6    
22.8    
23.0    
23.3    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.7    
27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
30.9    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
47.0    
47.2    
47.4    
47.7    
47.9    
48.1    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
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50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.6    
51.9    
52.1    
52.3    
52.6    
52.8    
53.0    
53.3    
53.5    
53.7    
54.0    
54.2    
54.4    
54.7    
54.9    
55.1    
55.3    
55.6    
55.8    
56.0    
56.3    
56.5    
56.7    
57.0    
57.2    
57.4    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.1    
59.3    
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59.8    
60.0    
60.2    
60.5    
60.7    
60.9    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
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64.9    
65.1    
65.3    
65.6    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.4    
68.6    
68.8    
69.1    
69.3    
69.5    
69.8    
70.0    
70.2    
70.5    
70.7    
70.9    
71.2    
71.4    
71.6    
71.9    
72.1    
72.3    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.7    
77.9    
78.1    
78.4    
78.6    
78.8    
79.1    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 45 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 45 predictions persist after filtering for low support