-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_9624356-9896184

-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_13-snap.1772-T1
Valid prediction for Augustus_model.g21461.t1
Valid prediction for GlimmerHMM_glimmerT_32187-T1
Valid prediction for snap_scaffold_13-snap.1773-T1
Valid prediction for snap_scaffold_13-snap.1768-T1
Valid prediction for snap_scaffold_13-snap.1779-T1
Valid prediction for Augustus_model.g21473.t1
Valid prediction for Augustus_model.g21476.t1
Valid prediction for GlimmerHMM_glimmerT_32167-T1
Valid prediction for GlimmerHMM_glimmerT_32184-T1
Valid prediction for Augustus_model.g21469.t1
Valid prediction for snap_scaffold_13-snap.1756-T1
Valid prediction for GlimmerHMM_glimmerT_32170-T1
Valid prediction for snap_scaffold_13-snap.1787-T1
Valid prediction for snap_scaffold_13-snap.1793-T1
Valid prediction for GlimmerHMM_glimmerT_32183-T1
Valid prediction for snap_scaffold_13-snap.1788-T1
Valid prediction for GlimmerHMM_glimmerT_32182-T1
Valid prediction for Augustus_model.g21468.t1
Valid prediction for snap_scaffold_13-snap.1781-T1
Valid prediction for snap_scaffold_13-snap.1775-T1
Valid prediction for snap_scaffold_13-snap.1783-T1
Valid prediction for Augustus_model.g21481.t1
Valid prediction for GlimmerHMM_glimmerT_32172-T1
Valid prediction for snap_scaffold_13-snap.1758-T1
Valid prediction for GlimmerHMM_glimmerT_32171-T1
Valid prediction for Augustus_model.g21465.t1
Valid prediction for snap_scaffold_13-snap.1789-T1
Valid prediction for Augustus_model.g21480.t1
Valid prediction for snap_scaffold_13-snap.1785-T1
Valid prediction for GlimmerHMM_glimmerT_32180-T1
Valid prediction for GlimmerHMM_glimmerT_32168-T1
Valid prediction for snap_scaffold_13-snap.1757-T1
Valid prediction for snap_scaffold_13-snap.1798-T1
Valid prediction for snap_scaffold_13-snap.1782-T1
Valid prediction for snap_scaffold_13-snap.1797-T1
Valid prediction for snap_scaffold_13-snap.1766-T1
Valid prediction for Augustus_model.g21482.t1
Valid prediction for snap_scaffold_13-snap.1761-T1
Valid prediction for snap_scaffold_13-snap.1760-T1
Valid prediction for Augustus_model.g21475.t1
Valid prediction for snap_scaffold_13-snap.1784-T1
Valid prediction for Augustus_model.g21472.t1
Valid prediction for snap_scaffold_13-snap.1774-T1
Valid prediction for Augustus_model.g21474.t1
Valid prediction for snap_scaffold_13-snap.1800-T1
Valid prediction for snap_scaffold_13-snap.1796-T1
Valid prediction for GlimmerHMM_glimmerT_32174-T1
Valid prediction for GlimmerHMM_glimmerT_32176-T1
Valid prediction for Augustus_model.g21466.t1
Valid prediction for GlimmerHMM_glimmerT_32186-T1
Valid prediction for snap_scaffold_13-snap.1799-T1
Valid prediction for snap_scaffold_13-snap.1771-T1
Valid prediction for GlimmerHMM_glimmerT_32179-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_13-snap.1753-T1
Valid prediction for Augustus_model.g21464.t1
Valid prediction for snap_scaffold_13-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_32177-T1
Valid prediction for snap_scaffold_13-snap.1795-T1
Valid prediction for GlimmerHMM_glimmerT_32164-T1
Valid prediction for Augustus_model.g21479.t1
Valid prediction for GlimmerHMM_glimmerT_32173-T1
Valid prediction for GlimmerHMM_glimmerT_32175-T1
Valid prediction for HiQ_model.g21470.t1
Valid prediction for Augustus_model.g21463.t1
Valid prediction for snap_scaffold_13-snap.1751-T1
Valid prediction for pasa_asmbl_10041.p1
Valid prediction for GlimmerHMM_glimmerT_32181-T1
Valid prediction for snap_scaffold_13-snap.1763-T1
Couldn't classify 263581, 263720
Couldn't classify 265933, 265967
Sorry, prediction pasa_asmbl_10040.p1 fails validation.
(ATA)	 GC	263581-263720	GT	AGG
(ATA)	 AG	264329-264465	GT	CAG
(ACA)	 AG	264600-264721	GT	AGG
(AGG)	 AG	265483-265600	GT	AGG
(ATA)	 AG	265933-265967	TA	GCT
-recovered pasa_asmbl_10040.p1, internal, 264329, 264465
-recovered pasa_asmbl_10040.p1, internal, 264600, 264721
-recovered pasa_asmbl_10040.p1, internal, 265483, 265600
Valid prediction for snap_scaffold_13-snap.1759-T1
Couldn't classify 267109, 267576
Sorry, prediction pasa_asmbl_10039.p1 fails validation.
(CTG)	 CG	267109-267576	CT	AGC
Valid prediction for Augustus_model.g21477.t1
Valid prediction for snap_scaffold_13-snap.1765-T1
Valid prediction for snap_scaffold_13-snap.1792-T1
Valid prediction for snap_scaffold_13-snap.1767-T1
Valid prediction for snap_scaffold_13-snap.1762-T1
Valid prediction for GlimmerHMM_glimmerT_32165-T1
Valid prediction for GlimmerHMM_glimmerT_32166-T1
Valid prediction for snap_scaffold_13-snap.1794-T1
Valid prediction for snap_scaffold_13-snap.1780-T1
Valid prediction for snap_scaffold_13-snap.1752-T1
Valid prediction for Augustus_model.g21460.t1
Valid prediction for snap_scaffold_13-snap.1755-T1
Valid prediction for snap_scaffold_13-snap.1790-T1
Valid prediction for snap_scaffold_13-snap.1769-T1
Valid prediction for snap_scaffold_13-snap.1791-T1
Valid prediction for Augustus_model.g21478.t1
Valid prediction for snap_scaffold_13-snap.1777-T1
Valid prediction for GlimmerHMM_glimmerT_32185-T1
Valid prediction for GlimmerHMM_glimmerT_32178-T1
Valid prediction for snap_scaffold_13-snap.1786-T1
Valid prediction for Augustus_model.g21459.t1
Valid prediction for snap_scaffold_13-snap.1770-T1
Valid prediction for snap_scaffold_13-snap.1778-T1
Valid prediction for GlimmerHMM_glimmerT_32169-T1
Valid prediction for snap_scaffold_13-snap.1776-T1
Valid prediction for Augustus_model.g21471.t1
Valid prediction for snap_scaffold_13-snap.1754-T1
Valid prediction for Augustus_model.g21462.t1
Valid prediction for Augustus_model.g21467.t1
Valid prediction for CodingQuarry_transcript_13215-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 137286, rend_intergenic: 137283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46521, rend_intergenic: 37669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54953, rend_intergenic: 52166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85652, rend_intergenic: 82790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105522, rend_intergenic: 102787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108512, rend_intergenic: 106760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137286, rend_intergenic: 134274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179044, rend_intergenic: 176719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199838, rend_intergenic: 197927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226959, rend_intergenic: 224720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232531, rend_intergenic: 231418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234999, rend_intergenic: 233299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244129, rend_intergenic: 242310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 271829
-exon list size: 383


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.9    
3.1    
3.4    
3.6    
3.9    
4.2    
4.4    
4.7    
4.9    
5.2    
5.5    
5.7    
6.0    
6.2    
6.5    
6.8    
7.0    
7.3    
7.5    
7.8    
8.1    
8.3    
8.6    
8.8    
9.1    
9.4    
9.6    
9.9    
10.1    
10.4    
10.6    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.5    
12.7    
13.0    
13.2    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.6    
21.8    
22.1    
22.3    
22.6    
22.9    
23.1    
23.4    
23.6    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.5    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.4    
36.6    
36.9    
37.1    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.9    
63.1    
63.4    
63.6    
63.9    
64.2    
64.4    
64.7    
64.9    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.1    
68.3    
68.6    
68.8    
69.1    
69.4    
69.6    
69.9    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.5    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.4    
76.6    
76.9    
77.1    
77.4    
77.7    
77.9    
78.2    
78.4    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.5    
92.7    
93.0    
93.2    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.4    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 36 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 137286, rend_intergenic: 137283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46521, rend_intergenic: 37669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54953, rend_intergenic: 52166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85652, rend_intergenic: 82790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105522, rend_intergenic: 102787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108512, rend_intergenic: 106760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137286, rend_intergenic: 134274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179044, rend_intergenic: 176719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199838, rend_intergenic: 197927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226959, rend_intergenic: 224720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232531, rend_intergenic: 231418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234999, rend_intergenic: 233299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244129, rend_intergenic: 242310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support