-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_2108753-2405548

-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_21718-T1
Valid prediction for GlimmerHMM_glimmerT_21704-T1
Valid prediction for GlimmerHMM_glimmerT_21731-T1
Valid prediction for snap_scaffold_9-snap.467-T1
Valid prediction for snap_scaffold_9-snap.482-T1
Valid prediction for snap_scaffold_9-snap.485-T1
Valid prediction for GlimmerHMM_glimmerT_21734-T1
Valid prediction for snap_scaffold_9-snap.461-T1
Valid prediction for snap_scaffold_9-snap.483-T1
Valid prediction for GlimmerHMM_glimmerT_21701-T1
Valid prediction for snap_scaffold_9-snap.489-T1
Valid prediction for Augustus_model.g14446.t1
Valid prediction for GlimmerHMM_glimmerT_21723-T1
Valid prediction for Augustus_model.g14445.t1
Valid prediction for GlimmerHMM_glimmerT_21730-T1
Valid prediction for snap_scaffold_9-snap.470-T1
Valid prediction for GlimmerHMM_glimmerT_21709-T1
Valid prediction for GlimmerHMM_glimmerT_21729-T1
Valid prediction for Augustus_model.g14450.t1
Valid prediction for GlimmerHMM_glimmerT_21719-T1
Valid prediction for Augustus_model.g14449.t1
Valid prediction for snap_scaffold_9-snap.477-T1
Valid prediction for snap_scaffold_9-snap.509-T1
Valid prediction for snap_scaffold_9-snap.498-T1
Valid prediction for GlimmerHMM_glimmerT_21713-T1
Valid prediction for GlimmerHMM_glimmerT_21728-T1
Valid prediction for Augustus_model.g14448.t1
Valid prediction for Augustus_model.g14443.t1
Valid prediction for snap_scaffold_9-snap.473-T1
Valid prediction for GlimmerHMM_glimmerT_21711-T1
Valid prediction for Augustus_model.g14447.t1
Valid prediction for snap_scaffold_9-snap.495-T1
Valid prediction for GlimmerHMM_glimmerT_21705-T1
Valid prediction for GlimmerHMM_glimmerT_21721-T1
Valid prediction for snap_scaffold_9-snap.487-T1
Valid prediction for GlimmerHMM_glimmerT_21717-T1
Valid prediction for GlimmerHMM_glimmerT_21706-T1
Valid prediction for snap_scaffold_9-snap.502-T1
Valid prediction for GlimmerHMM_glimmerT_21715-T1
Valid prediction for GlimmerHMM_glimmerT_21726-T1
Valid prediction for snap_scaffold_9-snap.465-T1
Valid prediction for snap_scaffold_9-snap.478-T1
Valid prediction for snap_scaffold_9-snap.492-T1
Valid prediction for Augustus_model.g14444.t1
Valid prediction for Augustus_model.g14440.t1
Valid prediction for snap_scaffold_9-snap.479-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 GlimmerHMM_glimmerT_21703-T1
Valid prediction for snap_scaffold_9-snap.491-T1
Valid prediction for Augustus_model.g14441.t1
Valid prediction for snap_scaffold_9-snap.488-T1
Valid prediction for GlimmerHMM_glimmerT_21710-T1
Valid prediction for snap_scaffold_9-snap.507-T1
Valid prediction for snap_scaffold_9-snap.501-T1
Valid prediction for snap_scaffold_9-snap.468-T1
Valid prediction for snap_scaffold_9-snap.504-T1
Valid prediction for snap_scaffold_9-snap.490-T1
Couldn't classify 227343, 227942
Sorry, prediction pasa_asmbl_54867.p1 fails validation.
(GAC)	 CA	227343-227942	CC	AAC
Valid prediction for Augustus_model.g14451.t1
Valid prediction for Augustus_model.g14438.t1
Valid prediction for snap_scaffold_9-snap.497-T1
Valid prediction for GlimmerHMM_glimmerT_21714-T1
Valid prediction for GlimmerHMM_glimmerT_21720-T1
Valid prediction for snap_scaffold_9-snap.475-T1
Valid prediction for GlimmerHMM_glimmerT_21725-T1
Valid prediction for GlimmerHMM_glimmerT_21708-T1
Valid prediction for snap_scaffold_9-snap.496-T1
Valid prediction for snap_scaffold_9-snap.464-T1
Valid prediction for snap_scaffold_9-snap.499-T1
Valid prediction for GlimmerHMM_glimmerT_21732-T1
Valid prediction for snap_scaffold_9-snap.500-T1
Valid prediction for Augustus_model.g14442.t1
Valid prediction for snap_scaffold_9-snap.462-T1
Valid prediction for snap_scaffold_9-snap.505-T1
Valid prediction for snap_scaffold_9-snap.460-T1
Valid prediction for snap_scaffold_9-snap.503-T1
Valid prediction for snap_scaffold_9-snap.480-T1
Valid prediction for GlimmerHMM_glimmerT_21712-T1
Valid prediction for snap_scaffold_9-snap.508-T1
Valid prediction for snap_scaffold_9-snap.506-T1
Valid prediction for snap_scaffold_9-snap.493-T1
Valid prediction for snap_scaffold_9-snap.484-T1
Couldn't classify 143125, 143427
Sorry, prediction pasa_asmbl_54673.p1 fails validation.
(ACC)	 CT	143125-143427	AG	AGA
Valid prediction for snap_scaffold_9-snap.494-T1
Valid prediction for GlimmerHMM_glimmerT_21707-T1
Valid prediction for GlimmerHMM_glimmerT_21702-T1
Valid prediction for snap_scaffold_9-snap.474-T1
Valid prediction for snap_scaffold_9-snap.481-T1
Valid prediction for GlimmerHMM_glimmerT_21722-T1
Valid prediction for snap_scaffold_9-snap.486-T1
Valid prediction for GlimmerHMM_glimmerT_21724-T1
Valid prediction for snap_scaffold_9-snap.463-T1
Valid prediction for GlimmerHMM_glimmerT_21727-T1
Valid prediction for snap_scaffold_9-snap.471-T1
Valid prediction for snap_scaffold_9-snap.476-T1
Valid prediction for snap_scaffold_9-snap.469-T1
Valid prediction for GlimmerHMM_glimmerT_21733-T1
Valid prediction for snap_scaffold_9-snap.466-T1
Valid prediction for GlimmerHMM_glimmerT_21716-T1
Valid prediction for Augustus_model.g14439.t1
Valid prediction for snap_scaffold_9-snap.472-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8946, rend_intergenic: 6160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33033, rend_intergenic: 9706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34724, rend_intergenic: 33095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35349, rend_intergenic: 34793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38769, rend_intergenic: 35883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42499, rend_intergenic: 39245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45220, rend_intergenic: 42652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55105, rend_intergenic: 45645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69443, rend_intergenic: 58468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81399, rend_intergenic: 69582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101589, rend_intergenic: 81443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106091, rend_intergenic: 103430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109756, rend_intergenic: 108186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117104, rend_intergenic: 116061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135453, rend_intergenic: 124756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138316, rend_intergenic: 135527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143897, rend_intergenic: 140886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146907, rend_intergenic: 144039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157400, rend_intergenic: 147417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197197, rend_intergenic: 173036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239108, rend_intergenic: 198652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 279974, rend_intergenic: 240059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 296796
-exon list size: 396


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
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3.0    
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3.5    
3.8    
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6.8    
7.0    
7.3    
7.5    
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8.0    
8.3    
8.5    
8.8    
9.0    
9.3    
9.5    
9.8    
10.1    
10.3    
10.6    
10.8    
11.1    
11.3    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.1    
13.3    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.1    
68.3    
68.6    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
93.0    
93.2    
93.5    
93.7    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
96.0    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 8946, rend_intergenic: 6160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33033, rend_intergenic: 9706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34724, rend_intergenic: 33095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35349, rend_intergenic: 34793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38769, rend_intergenic: 35883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42499, rend_intergenic: 39245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45220, rend_intergenic: 42652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55105, rend_intergenic: 45645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69443, rend_intergenic: 58468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81399, rend_intergenic: 69582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101589, rend_intergenic: 81443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106091, rend_intergenic: 103430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109756, rend_intergenic: 108186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117104, rend_intergenic: 116061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135453, rend_intergenic: 124756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138316, rend_intergenic: 135527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143897, rend_intergenic: 140886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146907, rend_intergenic: 144039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157400, rend_intergenic: 147417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197197, rend_intergenic: 173036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239108, rend_intergenic: 198652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 279974, rend_intergenic: 240059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21955
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-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 1 - 11527
-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 11558 - 21955
-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