-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_2350489-2556585

-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_3-snap.543-T1
Valid prediction for GlimmerHMM_glimmerT_6155-T1
Valid prediction for snap_scaffold_3-snap.557-T1
Valid prediction for snap_scaffold_3-snap.570-T1
Valid prediction for GlimmerHMM_glimmerT_6165-T1
Valid prediction for snap_scaffold_3-snap.542-T1
Valid prediction for Augustus_model.g4023.t1
Valid prediction for Augustus_model.g4025.t1
Valid prediction for GlimmerHMM_glimmerT_6172-T1
Valid prediction for snap_scaffold_3-snap.546-T1
Valid prediction for snap_scaffold_3-snap.573-T1
Valid prediction for Augustus_model.g4015.t1
Valid prediction for snap_scaffold_3-snap.551-T1
Valid prediction for snap_scaffold_3-snap.540-T1
Valid prediction for GlimmerHMM_glimmerT_6173-T1
Valid prediction for snap_scaffold_3-snap.578-T1
Valid prediction for snap_scaffold_3-snap.574-T1
Valid prediction for snap_scaffold_3-snap.539-T1
Valid prediction for snap_scaffold_3-snap.579-T1
Valid prediction for Augustus_model.g4017.t1
Valid prediction for GlimmerHMM_glimmerT_6171-T1
Valid prediction for Augustus_model.g4018.t1
Valid prediction for GlimmerHMM_glimmerT_6170-T1
Valid prediction for snap_scaffold_3-snap.569-T1
Valid prediction for GlimmerHMM_glimmerT_6166-T1
Valid prediction for GlimmerHMM_glimmerT_6158-T1
Valid prediction for GlimmerHMM_glimmerT_6162-T1
Valid prediction for GlimmerHMM_glimmerT_6174-T1
Valid prediction for snap_scaffold_3-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_6157-T1
Valid prediction for GlimmerHMM_glimmerT_6164-T1
Valid prediction for snap_scaffold_3-snap.548-T1
Valid prediction for GlimmerHMM_glimmerT_6153-T1
Valid prediction for snap_scaffold_3-snap.549-T1
Valid prediction for snap_scaffold_3-snap.554-T1
Valid prediction for GlimmerHMM_glimmerT_6152-T1
Valid prediction for snap_scaffold_3-snap.560-T1
Valid prediction for snap_scaffold_3-snap.559-T1
Valid prediction for GlimmerHMM_glimmerT_6154-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 snap_scaffold_3-snap.567-T1
Couldn't classify 77597, 78623
Sorry, prediction pasa_asmbl_38743.p1 fails validation.
(TCC)	 AG	77597-78623	GT	AGG
(GTC)	 AG	78797-78810	GT	AAG
-recovered pasa_asmbl_38743.p1, terminal, 78797, 78810
-recovered pasa_asmbl_38743.p1, internal, 77597, 78623
-recovered pasa_asmbl_38743.p1, internal, 78797, 78810
Valid prediction for Augustus_model.g4016.t1
Valid prediction for GlimmerHMM_glimmerT_6167-T1
Valid prediction for GlimmerHMM_glimmerT_6169-T1
Valid prediction for snap_scaffold_3-snap.577-T1
Valid prediction for snap_scaffold_3-snap.547-T1
Valid prediction for GlimmerHMM_glimmerT_6160-T1
Valid prediction for snap_scaffold_3-snap.572-T1
Valid prediction for Augustus_model.g4019.t1
Valid prediction for Augustus_model.g4013.t1
Valid prediction for Augustus_model.g4022.t1
Valid prediction for snap_scaffold_3-snap.576-T1
Valid prediction for GlimmerHMM_glimmerT_6168-T1
Valid prediction for snap_scaffold_3-snap.568-T1
Valid prediction for GlimmerHMM_glimmerT_6163-T1
Valid prediction for GlimmerHMM_glimmerT_6156-T1
Valid prediction for snap_scaffold_3-snap.553-T1
Valid prediction for snap_scaffold_3-snap.550-T1
Valid prediction for Augustus_model.g4014.t1
Valid prediction for Augustus_model.g4020.t1
Valid prediction for GlimmerHMM_glimmerT_6151-T1
Valid prediction for Augustus_model.g4024.t1
Valid prediction for GlimmerHMM_glimmerT_6161-T1
Valid prediction for GlimmerHMM_glimmerT_6159-T1
Valid prediction for snap_scaffold_3-snap.544-T1
Valid prediction for snap_scaffold_3-snap.545-T1
Valid prediction for snap_scaffold_3-snap.552-T1
Valid prediction for snap_scaffold_3-snap.563-T1
Valid prediction for snap_scaffold_3-snap.556-T1
Valid prediction for Augustus_model.g4021.t1
Valid prediction for snap_scaffold_3-snap.565-T1
Valid prediction for snap_scaffold_3-snap.541-T1
Valid prediction for snap_scaffold_3-snap.575-T1
Valid prediction for snap_scaffold_3-snap.538-T1
Valid prediction for snap_scaffold_3-snap.561-T1
Valid prediction for snap_scaffold_3-snap.558-T1
Valid prediction for snap_scaffold_3-snap.564-T1
Valid prediction for snap_scaffold_3-snap.555-T1
Valid prediction for snap_scaffold_3-snap.562-T1
Valid prediction for snap_scaffold_3-snap.566-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9153, rend_intergenic: 3874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9628, rend_intergenic: 9170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14753, rend_intergenic: 10176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17722, rend_intergenic: 16146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31442, rend_intergenic: 25575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33744, rend_intergenic: 32006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43012, rend_intergenic: 33756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53659, rend_intergenic: 43195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56799, rend_intergenic: 53954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61297, rend_intergenic: 57094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71252, rend_intergenic: 69214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87833, rend_intergenic: 84701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181766, rend_intergenic: 180243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195278, rend_intergenic: 188310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197516, rend_intergenic: 195651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206097
-exon list size: 328


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
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3.0    
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3.6    
3.9    
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4.5    
4.8    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.2    
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16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
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23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
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25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
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58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
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62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.2    
65.5    
65.8    
66.1    
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66.7    
67.0    
67.3    
67.6    
67.9    
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70.0    
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70.6    
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74.8    
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77.9    
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82.7    
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83.6    
83.9    
84.2    
84.5    
84.8    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 9153, rend_intergenic: 3874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9628, rend_intergenic: 9170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14753, rend_intergenic: 10176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17722, rend_intergenic: 16146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31442, rend_intergenic: 25575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33744, rend_intergenic: 32006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43012, rend_intergenic: 33756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53659, rend_intergenic: 43195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56799, rend_intergenic: 53954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61297, rend_intergenic: 57094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71252, rend_intergenic: 69214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87833, rend_intergenic: 84701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181766, rend_intergenic: 180243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195278, rend_intergenic: 188310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197516, rend_intergenic: 195651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support