-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_8579932-8880355

-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_2-snap.1702-T1
Valid prediction for GlimmerHMM_glimmerT_4218-T1
Valid prediction for GlimmerHMM_glimmerT_4189-T1
Valid prediction for snap_scaffold_2-snap.1713-T1
Valid prediction for GlimmerHMM_glimmerT_4211-T1
Valid prediction for Augustus_model.g2833.t1
Valid prediction for snap_scaffold_2-snap.1700-T1
Valid prediction for GlimmerHMM_glimmerT_4216-T1
Valid prediction for GlimmerHMM_glimmerT_4204-T1
Valid prediction for HiQ_model.g2840.t1
Valid prediction for CodingQuarry_transcript_28632-T1
Valid prediction for Augustus_model.g2834.t1
Valid prediction for Augustus_model.g2824.t1
Valid prediction for CodingQuarry_transcript_28630-T1
Valid prediction for snap_scaffold_2-snap.1703-T1
Valid prediction for GlimmerHMM_glimmerT_4214-T1
Valid prediction for GlimmerHMM_glimmerT_4196-T1
Valid prediction for GlimmerHMM_glimmerT_4194-T1
Valid prediction for pasa_asmbl_24652.p1
Valid prediction for GlimmerHMM_glimmerT_4192-T1
Valid prediction for CodingQuarry_transcript_28631-T1
Valid prediction for Augustus_model.g2822.t1
Valid prediction for Augustus_model.g2835.t1
Valid prediction for snap_scaffold_2-snap.1707-T1
Valid prediction for pasa_asmbl_24655.p2
Valid prediction for snap_scaffold_2-snap.1731-T1
Valid prediction for Augustus_model.g2839.t1
Valid prediction for Augustus_model.g2837.t1
Valid prediction for snap_scaffold_2-snap.1732-T1
Valid prediction for GlimmerHMM_glimmerT_4198-T1
Valid prediction for snap_scaffold_2-snap.1704-T1
Couldn't classify 276761, 276917
Couldn't classify 277256, 277382
Sorry, prediction pasa_asmbl_24646.p1 fails validation.
(ATG)	 GC	276223-276384	GT	AGG
(TAT)	 AG	276521-276644	GT	AGG
(GTT)	 AG	276761-276917	AT	AGA
(TTT)	 AC	277256-277382	TA	GGT
-recovered pasa_asmbl_24646.p1, initial, 276223, 276384
-recovered pasa_asmbl_24646.p1, terminal, 276761, 276917
-recovered pasa_asmbl_24646.p1, internal, 276521, 276644
Valid prediction for snap_scaffold_2-snap.1714-T1
Valid prediction for GlimmerHMM_glimmerT_4215-T1
Valid prediction for Augustus_model.g2836.t1
Valid prediction for GlimmerHMM_glimmerT_4213-T1
Valid prediction for GlimmerHMM_glimmerT_4190-T1
Valid prediction for GlimmerHMM_glimmerT_4201-T1
Valid prediction for snap_scaffold_2-snap.1699-T1
Valid prediction for snap_scaffold_2-snap.1706-T1
Valid prediction for snap_scaffold_2-snap.1737-T1
Valid prediction for snap_scaffold_2-snap.1708-T1
Valid prediction for snap_scaffold_2-snap.1716-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_2-snap.1723-T1
Valid prediction for GlimmerHMM_glimmerT_4191-T1
Valid prediction for Augustus_model.g2831.t1
Valid prediction for snap_scaffold_2-snap.1736-T1
Valid prediction for snap_scaffold_2-snap.1720-T1
Valid prediction for snap_scaffold_2-snap.1718-T1
Valid prediction for snap_scaffold_2-snap.1710-T1
Valid prediction for snap_scaffold_2-snap.1705-T1
Valid prediction for GlimmerHMM_glimmerT_4208-T1
Valid prediction for snap_scaffold_2-snap.1729-T1
Valid prediction for snap_scaffold_2-snap.1726-T1
Valid prediction for GlimmerHMM_glimmerT_4203-T1
Valid prediction for Augustus_model.g2832.t1
Valid prediction for GlimmerHMM_glimmerT_4207-T1
Valid prediction for Augustus_model.g2826.t1
Valid prediction for Augustus_model.g2827.t1
Valid prediction for snap_scaffold_2-snap.1722-T1
Valid prediction for snap_scaffold_2-snap.1712-T1
Valid prediction for GlimmerHMM_glimmerT_4210-T1
Valid prediction for Augustus_model.g2823.t1
Valid prediction for Augustus_model.g2828.t1
Valid prediction for GlimmerHMM_glimmerT_4195-T1
Valid prediction for GlimmerHMM_glimmerT_4205-T1
Valid prediction for snap_scaffold_2-snap.1734-T1
Valid prediction for snap_scaffold_2-snap.1727-T1
Valid prediction for snap_scaffold_2-snap.1715-T1
Valid prediction for GlimmerHMM_glimmerT_4193-T1
Valid prediction for Augustus_model.g2829.t1
Valid prediction for GlimmerHMM_glimmerT_4217-T1
Valid prediction for Augustus_model.g2821.t1
Valid prediction for GlimmerHMM_glimmerT_4209-T1
Valid prediction for Augustus_model.g2825.t1
Valid prediction for HiQ_model.g2830.t1
Valid prediction for pasa_asmbl_23332.p1
Valid prediction for snap_scaffold_2-snap.1733-T1
Valid prediction for GlimmerHMM_glimmerT_4212-T1
Valid prediction for snap_scaffold_2-snap.1735-T1
Valid prediction for GlimmerHMM_glimmerT_4206-T1
Valid prediction for CodingQuarry_transcript_28628-T1
Valid prediction for HiQ_model.g2838.t1
Valid prediction for GlimmerHMM_glimmerT_4202-T1
Valid prediction for CodingQuarry_transcript_28627-T1
Valid prediction for GlimmerHMM_glimmerT_4200-T1
Valid prediction for pasa_asmbl_23334.p1
Valid prediction for snap_scaffold_2-snap.1728-T1
Valid prediction for snap_scaffold_2-snap.1730-T1
Valid prediction for pasa_asmbl_23343.p1
Valid prediction for GlimmerHMM_glimmerT_4197-T1
Valid prediction for snap_scaffold_2-snap.1701-T1
Valid prediction for snap_scaffold_2-snap.1719-T1
Valid prediction for snap_scaffold_2-snap.1724-T1
Valid prediction for snap_scaffold_2-snap.1717-T1
Valid prediction for snap_scaffold_2-snap.1725-T1
Valid prediction for snap_scaffold_2-snap.1721-T1
Valid prediction for snap_scaffold_2-snap.1709-T1
Valid prediction for GlimmerHMM_glimmerT_4199-T1
Valid prediction for snap_scaffold_2-snap.1711-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 177292, rend_intergenic: 176510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183567, rend_intergenic: 179284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 284837, rend_intergenic: 283556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 300424
-exon list size: 282


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.2    
4.6    
4.9    
5.3    
5.6    
6.0    
6.3    
6.7    
7.0    
7.4    
7.7    
8.1    
8.5    
8.8    
9.2    
9.5    
9.9    
10.2    
10.6    
10.9    
11.3    
11.6    
12.0    
12.3    
12.7    
13.0    
13.4    
13.7    
14.1    
14.4    
14.8    
15.1    
15.5    
15.8    
16.2    
16.5    
16.9    
17.3    
17.6    
18.0    
18.3    
18.7    
19.0    
19.4    
19.7    
20.1    
20.4    
20.8    
21.1    
21.5    
21.8    
22.2    
22.5    
22.9    
23.2    
23.6    
23.9    
24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
26.4    
26.8    
27.1    
27.5    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
29.9    
30.3    
30.6    
31.0    
31.3    
31.7    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.5    
34.9    
35.2    
35.6    
35.9    
36.3    
36.6    
37.0    
37.3    
37.7    
38.0    
38.4    
38.7    
39.1    
39.4    
39.8    
40.1    
40.5    
40.8    
41.2    
41.5    
41.9    
42.3    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.7    
45.1    
45.4    
45.8    
46.1    
46.5    
46.8    
47.2    
47.5    
47.9    
48.2    
48.6    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.4    
51.8    
52.1    
52.5    
52.8    
53.2    
53.5    
53.9    
54.2    
54.6    
54.9    
55.3    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.7    
58.1    
58.5    
58.8    
59.2    
59.5    
59.9    
60.2    
60.6    
60.9    
61.3    
61.6    
62.0    
62.3    
62.7    
63.0    
63.4    
63.7    
64.1    
64.4    
64.8    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.3    
68.7    
69.0    
69.4    
69.7    
70.1    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.5    
72.9    
73.2    
73.6    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.4    
76.8    
77.1    
77.5    
77.8    
78.2    
78.5    
78.9    
79.2    
79.6    
79.9    
80.3    
80.6    
81.0    
81.3    
81.7    
82.0    
82.4    
82.7    
83.1    
83.5    
83.8    
84.2    
84.5    
84.9    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.3    
87.7    
88.0    
88.4    
88.7    
89.1    
89.4    
89.8    
90.1    
90.5    
90.8    
91.2    
91.5    
91.9    
92.3    
92.6    
93.0    
93.3    
93.7    
94.0    
94.4    
94.7    
95.1    
95.4    
95.8    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 177292, rend_intergenic: 176510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183567, rend_intergenic: 179284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 284837, rend_intergenic: 283556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 43323
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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

-building DP trellis

-building trellis in range 1 - 42388
-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 - 27972
-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 1 - 21017
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 2652 - 21017
-exon list size: 1


building trellis

33.3    
66.7    
-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 27980 - 42388
-exon list size: 1


building trellis

33.3    
66.7    
-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