-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_6345729-6594158

-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_15-snap.1373-T1
Valid prediction for snap_scaffold_15-snap.1361-T1
Valid prediction for GlimmerHMM_glimmerT_36332-T1
Valid prediction for snap_scaffold_15-snap.1392-T1
Valid prediction for snap_scaffold_15-snap.1364-T1
Valid prediction for snap_scaffold_15-snap.1362-T1
Valid prediction for snap_scaffold_15-snap.1375-T1
Valid prediction for GlimmerHMM_glimmerT_36316-T1
Valid prediction for snap_scaffold_15-snap.1403-T1
Valid prediction for Augustus_model.g24197.t1
Couldn't classify 184950, 184960
Sorry, prediction pasa_asmbl_15254.p1 fails validation.
(ATG)	 AA	183235-183541	GT	CGG
(AGA)	 AG	184579-184719	GT	AGG
(ATG)	 AG	184950-184960	AC	ACA
-recovered pasa_asmbl_15254.p1, initial, 183235, 183541
-recovered pasa_asmbl_15254.p1, internal, 184579, 184719
Valid prediction for snap_scaffold_15-snap.1390-T1
Valid prediction for GlimmerHMM_glimmerT_36310-T1
Valid prediction for snap_scaffold_15-snap.1389-T1
Valid prediction for snap_scaffold_15-snap.1384-T1
Valid prediction for snap_scaffold_15-snap.1398-T1
Valid prediction for CodingQuarry_transcript_18026-T1
Valid prediction for GlimmerHMM_glimmerT_36328-T1
Valid prediction for GlimmerHMM_glimmerT_36327-T1
Valid prediction for snap_scaffold_15-snap.1393-T1
Valid prediction for HiQ_model.g24196.t1
Valid prediction for snap_scaffold_15-snap.1399-T1
Valid prediction for snap_scaffold_15-snap.1382-T1
Valid prediction for GlimmerHMM_glimmerT_36314-T1
Valid prediction for snap_scaffold_15-snap.1401-T1
Valid prediction for Augustus_model.g24193.t1
Valid prediction for GlimmerHMM_glimmerT_36329-T1
Valid prediction for HiQ_model.g24195.t1
Valid prediction for snap_scaffold_15-snap.1374-T1
Valid prediction for GlimmerHMM_glimmerT_36317-T1
Valid prediction for pasa_asmbl_15252.p1
Valid prediction for snap_scaffold_15-snap.1378-T1
Valid prediction for GlimmerHMM_glimmerT_36326-T1
Valid prediction for pasa_asmbl_15251.p1
Valid prediction for snap_scaffold_15-snap.1366-T1
Valid prediction for snap_scaffold_15-snap.1381-T1
Valid prediction for snap_scaffold_15-snap.1369-T1
Valid prediction for GlimmerHMM_glimmerT_36318-T1
Valid prediction for GlimmerHMM_glimmerT_36324-T1
Valid prediction for snap_scaffold_15-snap.1386-T1
Valid prediction for snap_scaffold_15-snap.1380-T1
Valid prediction for snap_scaffold_15-snap.1368-T1
Valid prediction for GlimmerHMM_glimmerT_36312-T1
Valid prediction for GlimmerHMM_glimmerT_36309-T1
Valid prediction for GlimmerHMM_glimmerT_36319-T1
Valid prediction for GlimmerHMM_glimmerT_36330-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_15-snap.1376-T1
Valid prediction for snap_scaffold_15-snap.1397-T1
Valid prediction for GlimmerHMM_glimmerT_36331-T1
Valid prediction for snap_scaffold_15-snap.1396-T1
Valid prediction for GlimmerHMM_glimmerT_36333-T1
Valid prediction for snap_scaffold_15-snap.1400-T1
Valid prediction for snap_scaffold_15-snap.1402-T1
Valid prediction for GlimmerHMM_glimmerT_36311-T1
Valid prediction for snap_scaffold_15-snap.1394-T1
Valid prediction for Augustus_model.g24200.t1
Valid prediction for GlimmerHMM_glimmerT_36323-T1
Valid prediction for GlimmerHMM_glimmerT_36313-T1
Valid prediction for GlimmerHMM_glimmerT_36320-T1
Valid prediction for GlimmerHMM_glimmerT_36321-T1
Valid prediction for GlimmerHMM_glimmerT_36325-T1
Valid prediction for Augustus_model.g24194.t1
Valid prediction for snap_scaffold_15-snap.1363-T1
Valid prediction for Augustus_model.g24191.t1
Valid prediction for snap_scaffold_15-snap.1391-T1
Valid prediction for snap_scaffold_15-snap.1367-T1
Valid prediction for Augustus_model.g24190.t1
Valid prediction for GlimmerHMM_glimmerT_36315-T1
Valid prediction for snap_scaffold_15-snap.1383-T1
Valid prediction for Augustus_model.g24192.t1
Valid prediction for snap_scaffold_15-snap.1372-T1
Valid prediction for GlimmerHMM_glimmerT_36334-T1
Valid prediction for snap_scaffold_15-snap.1395-T1
Valid prediction for snap_scaffold_15-snap.1365-T1
Valid prediction for snap_scaffold_15-snap.1385-T1
Valid prediction for Augustus_model.g24198.t1
Valid prediction for snap_scaffold_15-snap.1387-T1
Valid prediction for snap_scaffold_15-snap.1388-T1
Valid prediction for snap_scaffold_15-snap.1371-T1
Valid prediction for snap_scaffold_15-snap.1379-T1
Valid prediction for GlimmerHMM_glimmerT_36322-T1
Valid prediction for snap_scaffold_15-snap.1370-T1
Valid prediction for snap_scaffold_15-snap.1377-T1
Valid prediction for Augustus_model.g24199.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10109, rend_intergenic: 4862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20968, rend_intergenic: 10456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22285, rend_intergenic: 21091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25354, rend_intergenic: 22434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26745, rend_intergenic: 25460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38540, rend_intergenic: 27631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49790, rend_intergenic: 40346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71911, rend_intergenic: 52252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96304, rend_intergenic: 72161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112466, rend_intergenic: 107697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125275, rend_intergenic: 112601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127567, rend_intergenic: 125369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136883, rend_intergenic: 128888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138625, rend_intergenic: 137177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141085, rend_intergenic: 140712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142869, rend_intergenic: 141846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155854, rend_intergenic: 152214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175214, rend_intergenic: 170549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183867, rend_intergenic: 182522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216420, rend_intergenic: 215215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248430
-exon list size: 347


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
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3.4    
3.7    
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4.6    
4.9    
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5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
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26.4    
26.6    
26.9    
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27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 10109, rend_intergenic: 4862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20968, rend_intergenic: 10456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22285, rend_intergenic: 21091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25354, rend_intergenic: 22434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26745, rend_intergenic: 25460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38540, rend_intergenic: 27631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49790, rend_intergenic: 40346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71911, rend_intergenic: 52252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96304, rend_intergenic: 72161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112466, rend_intergenic: 107697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125275, rend_intergenic: 112601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127567, rend_intergenic: 125369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136883, rend_intergenic: 128888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138625, rend_intergenic: 137177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141085, rend_intergenic: 140712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142869, rend_intergenic: 141846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155854, rend_intergenic: 152214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175214, rend_intergenic: 170549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183867, rend_intergenic: 182522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216420, rend_intergenic: 215215  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

-building DP trellis

-building trellis in range 232587 - 248430
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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 232587 - 242988
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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