-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_9371834-9620705

-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.1776_t
Valid prediction for Augustus_model.g984.t1
Valid prediction for Augustus_model.g972.t1
Valid prediction for GlimmerHMM_glimmerT_1362-T1
Valid prediction for GlimmerHMM_glimmerT_1367-T1
Valid prediction for Augustus_model.g986.t1
Valid prediction for GeneMark_model.1796_t
Valid prediction for snap_scaffold_1-snap.1706-T1
Valid prediction for snap_scaffold_1-snap.1712-T1
Valid prediction for Augustus_model.g975.t1
Valid prediction for GlimmerHMM_glimmerT_1355-T1
Valid prediction for Augustus_model.g978.t1
Valid prediction for GlimmerHMM_glimmerT_1365-T1
Valid prediction for snap_scaffold_1-snap.1698-T1
Valid prediction for GeneMark_model.1800_t
Valid prediction for GeneMark_model.1798_t
Valid prediction for snap_scaffold_1-snap.1708-T1
Valid prediction for snap_scaffold_1-snap.1720-T1
Valid prediction for snap_scaffold_1-snap.1701-T1
Valid prediction for snap_scaffold_1-snap.1707-T1
Valid prediction for GeneMark_model.1802_t
Valid prediction for snap_scaffold_1-snap.1723-T1
Valid prediction for snap_scaffold_1-snap.1705-T1
Valid prediction for GeneMark_model.1794_t
Valid prediction for GlimmerHMM_glimmerT_1364-T1
Valid prediction for snap_scaffold_1-snap.1696-T1
Valid prediction for GlimmerHMM_glimmerT_1358-T1
Valid prediction for GeneMark_model.1784_t
Valid prediction for snap_scaffold_1-snap.1718-T1
Valid prediction for GeneMark_model.1805_t
Valid prediction for GeneMark_model.1780_t
Valid prediction for Augustus_model.g977.t1
Valid prediction for Augustus_model.g976.t1
Valid prediction for GeneMark_model.1785_t
Valid prediction for snap_scaffold_1-snap.1703-T1
Valid prediction for GlimmerHMM_glimmerT_1377-T1
Valid prediction for GeneMark_model.1782_t
Valid prediction for snap_scaffold_1-snap.1715-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_1357-T1
Valid prediction for snap_scaffold_1-snap.1697-T1
Valid prediction for snap_scaffold_1-snap.1717-T1
Valid prediction for GeneMark_model.1773_t
Valid prediction for GeneMark_model.1779_t
Valid prediction for Augustus_model.g973.t1
Valid prediction for GeneMark_model.1788_t

-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 Augustus_model.g983.t1
Valid prediction for GeneMark_model.1778_t
Valid prediction for Augustus_model.g981.t1
Valid prediction for GlimmerHMM_glimmerT_1360-T1
Valid prediction for GlimmerHMM_glimmerT_1359-T1
Valid prediction for GlimmerHMM_glimmerT_1356-T1
Valid prediction for pasa_asmbl_552.p1
Valid prediction for pasa_asmbl_547.p1
Valid prediction for Augustus_model.g987.t1
Valid prediction for GlimmerHMM_glimmerT_1376-T1
Valid prediction for snap_scaffold_1-snap.1711-T1
Valid prediction for snap_scaffold_1-snap.1713-T1
Valid prediction for GlimmerHMM_glimmerT_1373-T1
Valid prediction for HiQ_model.g980.t1
Valid prediction for GeneMark_model.1775_t
Valid prediction for snap_scaffold_1-snap.1722-T1
Valid prediction for snap_scaffold_1-snap.1719-T1
Valid prediction for GlimmerHMM_glimmerT_1368-T1
Valid prediction for snap_scaffold_1-snap.1714-T1
Valid prediction for GeneMark_model.1774_t
Valid prediction for GeneMark_model.1790_t
Valid prediction for GeneMark_model.1792_t
Valid prediction for GeneMark_model.1777_t
Valid prediction for GlimmerHMM_glimmerT_1366-T1
Valid prediction for Augustus_model.g990.t1
Valid prediction for GeneMark_model.1799_t
Valid prediction for snap_scaffold_1-snap.1716-T1
Valid prediction for GeneMark_model.1797_t
Valid prediction for GeneMark_model.1801_t
Valid prediction for snap_scaffold_1-snap.1721-T1
Valid prediction for snap_scaffold_1-snap.1702-T1
Valid prediction for GeneMark_model.1793_t
Couldn't classify 200285, 200403
Sorry, prediction pasa_asmbl_1277.p1 fails validation.
(ATG)	 CA	198928-198948	GT	GGG
(CAA)	 AG	199522-199679	GT	AGG
(AAG)	 AG	199955-200022	GT	CAG
(CCA)	 AG	200285-200403	GA	GTG
-recovered pasa_asmbl_1277.p1, initial, 198928, 198948
-recovered pasa_asmbl_1277.p1, internal, 199522, 199679
-recovered pasa_asmbl_1277.p1, internal, 199955, 200022
Valid prediction for Augustus_model.g974.t1
Valid prediction for GeneMark_model.1803_t
Valid prediction for snap_scaffold_1-snap.1704-T1
Valid prediction for GeneMark_model.1783_t
Valid prediction for snap_scaffold_1-snap.1699-T1
Valid prediction for Augustus_model.g985.t1
Valid prediction for Augustus_model.g982.t1
Valid prediction for CodingQuarry_transcript_2730-T1
Valid prediction for GeneMark_model.1786_t
Valid prediction for GlimmerHMM_glimmerT_1363-T1
Valid prediction for GeneMark_model.1791_t
Valid prediction for GeneMark_model.1795_t
Valid prediction for snap_scaffold_1-snap.1700-T1
Valid prediction for snap_scaffold_1-snap.1709-T1
Valid prediction for Augustus_model.g989.t1
Valid prediction for GlimmerHMM_glimmerT_1370-T1
Valid prediction for GlimmerHMM_glimmerT_1372-T1
Valid prediction for snap_scaffold_1-snap.1710-T1
Valid prediction for GlimmerHMM_glimmerT_1374-T1
Valid prediction for snap_scaffold_1-snap.1725-T1
Valid prediction for GeneMark_model.1787_t
Valid prediction for GeneMark_model.1804_t
Valid prediction for GlimmerHMM_glimmerT_1361-T1
Valid prediction for GlimmerHMM_glimmerT_1375-T1
Valid prediction for GlimmerHMM_glimmerT_1371-T1
Valid prediction for GeneMark_model.1806_t
Valid prediction for pasa_asmbl_544.p1
Valid prediction for snap_scaffold_1-snap.1724-T1
Valid prediction for snap_scaffold_1-snap.1726-T1
Valid prediction for HiQ_model.g979.t1
Valid prediction for GeneMark_model.1781_t
Valid prediction for GlimmerHMM_glimmerT_1369-T1
Valid prediction for Augustus_model.g988.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 64278, rend_intergenic: 63944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87791, rend_intergenic: 84245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171146, rend_intergenic: 164903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180039, rend_intergenic: 172367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187549, rend_intergenic: 185475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204387, rend_intergenic: 196596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248872
-exon list size: 470


building trellis

0.2    
0.4    
0.6    
0.8    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.2    
4.4    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 64278, rend_intergenic: 63944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87791, rend_intergenic: 84245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171146, rend_intergenic: 164903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180039, rend_intergenic: 172367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187549, rend_intergenic: 185475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204387, rend_intergenic: 196596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 18069
-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 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17676
-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 1 - 17547
-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

-building DP trellis

-building trellis in range 2101 - 17547
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 235545 - 248872
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support