-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_2513478-2653356

-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.78085_t
Valid prediction for GlimmerHMM_glimmerT_44769-T1
Valid prediction for snap_scaffold_19-snap.557-T1
Valid prediction for GeneMark_model.78059_t
Valid prediction for CodingQuarry_transcript_25549-T1
Valid prediction for GeneMark_model.78080_t
Valid prediction for snap_scaffold_19-snap.548-T1
Valid prediction for snap_scaffold_19-snap.573-T1
Valid prediction for pasa_asmbl_22069.p2
Valid prediction for GeneMark_model.78077_t
Valid prediction for GeneMark_model.78056_t
Valid prediction for snap_scaffold_19-snap.556-T1
Valid prediction for HiQ_model.g29878.t1
Valid prediction for GeneMark_model.78076_t
Valid prediction for GlimmerHMM_glimmerT_44771-T1
Valid prediction for snap_scaffold_19-snap.577-T1
Valid prediction for snap_scaffold_19-snap.554-T1
Valid prediction for Augustus_model.g29872.t1
Valid prediction for Augustus_model.g29876.t1
Valid prediction for GlimmerHMM_glimmerT_44758-T1
Valid prediction for Augustus_model.g29874.t1
Valid prediction for snap_scaffold_19-snap.569-T1
Valid prediction for GeneMark_model.78064_t
Valid prediction for GeneMark_model.78051_t
Valid prediction for GlimmerHMM_glimmerT_44775-T1
Valid prediction for snap_scaffold_19-snap.545-T1
Valid prediction for snap_scaffold_19-snap.565-T1
Valid prediction for GlimmerHMM_glimmerT_44773-T1
Valid prediction for GeneMark_model.78066_t
Valid prediction for GlimmerHMM_glimmerT_44761-T1
Valid prediction for GlimmerHMM_glimmerT_44767-T1
Valid prediction for GlimmerHMM_glimmerT_44760-T1
Valid prediction for GeneMark_model.78082_t
Valid prediction for GeneMark_model.78061_t
Valid prediction for GlimmerHMM_glimmerT_44774-T1
Valid prediction for GlimmerHMM_glimmerT_44768-T1
Valid prediction for snap_scaffold_19-snap.567-T1
Valid prediction for snap_scaffold_19-snap.559-T1
Valid prediction for GeneMark_model.78088_t
Valid prediction for snap_scaffold_19-snap.584-T1
Valid prediction for Augustus_model.g29870.t1
Valid prediction for Augustus_model.g29875.t1
Valid prediction for snap_scaffold_19-snap.551-T1
Valid prediction for snap_scaffold_19-snap.560-T1
Valid prediction for GlimmerHMM_glimmerT_44764-T1
Valid prediction for GeneMark_model.78063_t
Valid prediction for GlimmerHMM_glimmerT_44766-T1
Valid prediction for snap_scaffold_19-snap.581-T1
Valid prediction for GeneMark_model.78054_t
Valid prediction for Augustus_model.g29871.t1
Valid prediction for GeneMark_model.78067_t
Valid prediction for GeneMark_model.78052_t
Valid prediction for GeneMark_model.78071_t
Valid prediction for GeneMark_model.78053_t
Valid prediction for snap_scaffold_19-snap.546-T1
Valid prediction for GeneMark_model.78050_t
Valid prediction for GeneMark_model.78073_t
Valid prediction for snap_scaffold_19-snap.547-T1
Valid prediction for GeneMark_model.78079_t
Valid prediction for Augustus_model.g29877.t1
Valid prediction for snap_scaffold_19-snap.574-T1
Valid prediction for GeneMark_model.78057_t
Valid prediction for snap_scaffold_19-snap.579-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_19-snap.582-T1
Valid prediction for GlimmerHMM_glimmerT_44762-T1
Valid prediction for GeneMark_model.78078_t
Valid prediction for GeneMark_model.78087_t
Valid prediction for snap_scaffold_19-snap.566-T1
Valid prediction for snap_scaffold_19-snap.580-T1
Valid prediction for GlimmerHMM_glimmerT_44759-T1
Valid prediction for snap_scaffold_19-snap.555-T1
Valid prediction for GeneMark_model.78069_t
Valid prediction for snap_scaffold_19-snap.572-T1
Valid prediction for GeneMark_model.78074_t
Valid prediction for GlimmerHMM_glimmerT_44763-T1
Valid prediction for snap_scaffold_19-snap.564-T1
Valid prediction for snap_scaffold_19-snap.576-T1
Valid prediction for snap_scaffold_19-snap.558-T1
Valid prediction for GeneMark_model.78070_t
Valid prediction for GeneMark_model.78060_t
Valid prediction for GeneMark_model.78084_t
Valid prediction for snap_scaffold_19-snap.571-T1
Valid prediction for snap_scaffold_19-snap.570-T1
Valid prediction for snap_scaffold_19-snap.562-T1
Valid prediction for snap_scaffold_19-snap.575-T1
Valid prediction for snap_scaffold_19-snap.552-T1
Valid prediction for GeneMark_model.78058_t
Valid prediction for GeneMark_model.78068_t
Valid prediction for GlimmerHMM_glimmerT_44770-T1
Valid prediction for GeneMark_model.78062_t
Valid prediction for Augustus_model.g29869.t1
Valid prediction for Augustus_model.g29873.t1
Valid prediction for GeneMark_model.78065_t
Valid prediction for snap_scaffold_19-snap.583-T1
Valid prediction for snap_scaffold_19-snap.553-T1
Valid prediction for snap_scaffold_19-snap.549-T1
Valid prediction for snap_scaffold_19-snap.568-T1
Valid prediction for GeneMark_model.78081_t
Valid prediction for snap_scaffold_19-snap.563-T1
Valid prediction for snap_scaffold_19-snap.550-T1
Valid prediction for snap_scaffold_19-snap.561-T1
Valid prediction for GeneMark_model.78083_t
Valid prediction for GeneMark_model.78055_t
Valid prediction for GlimmerHMM_glimmerT_44772-T1
Valid prediction for snap_scaffold_19-snap.578-T1
Valid prediction for GeneMark_model.78049_t
Valid prediction for GeneMark_model.78075_t
Valid prediction for GlimmerHMM_glimmerT_44765-T1
Valid prediction for GeneMark_model.78072_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 17799, rend_intergenic: 17796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22673, rend_intergenic: 20969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28197, rend_intergenic: 23568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32043, rend_intergenic: 28420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35806, rend_intergenic: 32370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54596, rend_intergenic: 53749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69354, rend_intergenic: 58836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73656, rend_intergenic: 71098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77163, rend_intergenic: 73737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86084, rend_intergenic: 83640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94096, rend_intergenic: 92258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101345, rend_intergenic: 98123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112160, rend_intergenic: 102856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113064, rend_intergenic: 112429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115671, rend_intergenic: 113231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118098, rend_intergenic: 116541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127778, rend_intergenic: 127399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129566, rend_intergenic: 127782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 139879
-exon list size: 567


building trellis

0.2    
0.4    
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0.9    
1.1    
1.2    
1.4    
1.6    
1.8    
1.9    
2.1    
2.3    
2.5    
2.6    
2.8    
3.0    
3.2    
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3.5    
3.7    
3.9    
4.0    
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4.6    
4.7    
4.9    
5.1    
5.3    
5.4    
5.6    
5.8    
6.0    
6.2    
6.3    
6.5    
6.7    
6.9    
7.0    
7.2    
7.4    
7.6    
7.7    
7.9    
8.1    
8.3    
8.4    
8.6    
8.8    
9.0    
9.1    
9.3    
9.5    
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9.8    
10.0    
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10.4    
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10.9    
11.1    
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11.8    
12.0    
12.1    
12.3    
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13.9    
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15.8    
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17.0    
17.2    
17.4    
17.6    
17.8    
17.9    
18.1    
18.3    
18.5    
18.6    
18.8    
19.0    
19.2    
19.3    
19.5    
19.7    
19.9    
20.0    
20.2    
20.4    
20.6    
20.7    
20.9    
21.1    
21.3    
21.4    
21.6    
21.8    
22.0    
22.1    
22.3    
22.5    
22.7    
22.8    
23.0    
23.2    
23.4    
23.6    
23.7    
23.9    
24.1    
24.3    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.8    
26.0    
26.2    
26.4    
26.5    
26.7    
26.9    
27.1    
27.2    
27.4    
27.6    
27.8    
27.9    
28.1    
28.3    
28.5    
28.6    
28.8    
29.0    
29.2    
29.3    
29.5    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.8    
30.9    
31.1    
31.3    
31.5    
31.6    
31.8    
32.0    
32.2    
32.3    
32.5    
32.7    
32.9    
33.0    
33.2    
33.4    
33.6    
33.7    
33.9    
34.1    
34.3    
34.4    
34.6    
34.8    
35.0    
35.1    
35.3    
35.5    
35.7    
35.9    
36.0    
36.2    
36.4    
36.6    
36.7    
36.9    
37.1    
37.3    
37.4    
37.6    
37.8    
38.0    
38.1    
38.3    
38.5    
38.7    
38.8    
39.0    
39.2    
39.4    
39.5    
39.7    
39.9    
40.1    
40.2    
40.4    
40.6    
40.8    
40.9    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.4    
42.5    
42.7    
42.9    
43.1    
43.2    
43.4    
43.6    
43.8    
43.9    
44.1    
44.3    
44.5    
44.6    
44.8    
45.0    
45.2    
45.3    
45.5    
45.7    
45.9    
46.0    
46.2    
46.4    
46.6    
46.7    
46.9    
47.1    
47.3    
47.5    
47.6    
47.8    
48.0    
48.2    
48.3    
48.5    
48.7    
48.9    
49.0    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
51.0    
51.1    
51.3    
51.5    
51.7    
51.8    
52.0    
52.2    
52.4    
52.5    
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52.9    
53.1    
53.3    
53.4    
53.6    
53.8    
54.0    
54.1    
54.3    
54.5    
54.7    
54.8    
55.0    
55.2    
55.4    
55.5    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.5    
57.6    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.1    
59.2    
59.4    
59.6    
59.8    
59.9    
60.1    
60.3    
60.5    
60.6    
60.8    
61.0    
61.2    
61.3    
61.5    
61.7    
61.9    
62.0    
62.2    
62.4    
62.6    
62.7    
62.9    
63.1    
63.3    
63.4    
63.6    
63.8    
64.0    
64.1    
64.3    
64.5    
64.7    
64.9    
65.0    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.5    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.8    
85.9    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 17799, rend_intergenic: 17796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22673, rend_intergenic: 20969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28197, rend_intergenic: 23568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32043, rend_intergenic: 28420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35806, rend_intergenic: 32370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54596, rend_intergenic: 53749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69354, rend_intergenic: 58836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73656, rend_intergenic: 71098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77163, rend_intergenic: 73737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86084, rend_intergenic: 83640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94096, rend_intergenic: 92258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101345, rend_intergenic: 98123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112160, rend_intergenic: 102856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113064, rend_intergenic: 112429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115671, rend_intergenic: 113231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118098, rend_intergenic: 116541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127778, rend_intergenic: 127399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129566, rend_intergenic: 127782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support