-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_3163878-3341890

-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: +)Couldn't classify 147463, 147531
Couldn't classify 154096, 154518
Sorry, prediction pasa_asmbl_51741.p1 fails validation.
(GAG)	 CA	147463-147531	GT	AGG
(GAT)	 AG	148036-148141	GT	AGG
(CCC)	 AG	150415-150509	GT	TGG
(TCC)	 AG	151262-151373	GT	AGG
(GTG)	 AG	151827-151921	GT	AGG
(ACC)	 AG	152695-152838	GT	AGG
(GCT)	 AG	154096-154518	TA	CGT
-recovered pasa_asmbl_51741.p1, internal, 148036, 148141
-recovered pasa_asmbl_51741.p1, internal, 150415, 150509
-recovered pasa_asmbl_51741.p1, internal, 151262, 151373
-recovered pasa_asmbl_51741.p1, internal, 151827, 151921
-recovered pasa_asmbl_51741.p1, internal, 152695, 152838
Valid prediction for GeneMark_model.34019_t
Valid prediction for snap_scaffold_8-snap.621-T1
Valid prediction for snap_scaffold_8-snap.635-T1
Valid prediction for snap_scaffold_8-snap.623-T1
Valid prediction for GlimmerHMM_glimmerT_19886-T1
Valid prediction for GeneMark_model.34025_t
Valid prediction for snap_scaffold_8-snap.618-T1
Valid prediction for GeneMark_model.34011_t
Valid prediction for snap_scaffold_8-snap.637-T1
Valid prediction for GlimmerHMM_glimmerT_19899-T1
Valid prediction for snap_scaffold_8-snap.634-T1
Valid prediction for GeneMark_model.34003_t
Valid prediction for GeneMark_model.34014_t
Valid prediction for GeneMark_model.34016_t
Valid prediction for GeneMark_model.33997_t
Valid prediction for GeneMark_model.34027_t
Valid prediction for snap_scaffold_8-snap.629-T1
Valid prediction for GlimmerHMM_glimmerT_19892-T1
Couldn't classify 168858, 169120
Sorry, prediction pasa_asmbl_51743.p1 fails validation.
(ATG)	 AT	163172-163200	GT	GCG
(AGA)	 AG	165110-165270	GT	AGG
(CTT)	 AG	167383-167520	GC	AGG
(GTG)	 AG	168858-169120	GA	AGG
-recovered pasa_asmbl_51743.p1, initial, 163172, 163200
-recovered pasa_asmbl_51743.p1, internal, 165110, 165270
-recovered pasa_asmbl_51743.p1, internal, 167383, 167520
Valid prediction for GlimmerHMM_glimmerT_19895-T1
Valid prediction for GeneMark_model.34031_t
Valid prediction for GlimmerHMM_glimmerT_19888-T1
Valid prediction for GeneMark_model.34001_t
Valid prediction for GeneMark_model.34005_t
Valid prediction for GeneMark_model.33995_t
Valid prediction for snap_scaffold_8-snap.610-T1
Valid prediction for snap_scaffold_8-snap.633-T1
Valid prediction for snap_scaffold_8-snap.615-T1
Valid prediction for GeneMark_model.34028_t
Valid prediction for HiQ_model.g13301.t1
Valid prediction for GeneMark_model.34033_t
Valid prediction for GeneMark_model.34013_t
Couldn't classify 169636, 169806
Couldn't classify 175075, 175221
Sorry, prediction pasa_asmbl_52638.p1 fails validation.
(AAA)	 AG	169636-169806	GT	AGG
(AAA)	 AG	170567-170722	GT	AGG
(AAG)	 AG	171233-171415	GT	AGG
(GAG)	 AG	172080-172199	GT	GCG
(GCC)	 AG	173028-173189	GC	AGG
(GTG)	 AG	173755-173945	GT	AGG
(GTT)	 AG	174640-174832	GT	AGG
(ACT)	 AG	175075-175221	CG	GCC
-recovered pasa_asmbl_52638.p1, internal, 169636, 169806
-recovered pasa_asmbl_52638.p1, internal, 170567, 170722
-recovered pasa_asmbl_52638.p1, internal, 171233, 171415
-recovered pasa_asmbl_52638.p1, internal, 172080, 172199
-recovered pasa_asmbl_52638.p1, internal, 173028, 173189
-recovered pasa_asmbl_52638.p1, internal, 173755, 173945
-recovered pasa_asmbl_52638.p1, internal, 174640, 174832
Valid prediction for GeneMark_model.34006_t
Valid prediction for GlimmerHMM_glimmerT_19898-T1
Valid prediction for snap_scaffold_8-snap.638-T1
Valid prediction for snap_scaffold_8-snap.616-T1
Valid prediction for HiQ_model.g13302.t1
Valid prediction for GlimmerHMM_glimmerT_19891-T1
Valid prediction for Augustus_model.g13299.t1
Valid prediction for GeneMark_model.34021_t
Valid prediction for GlimmerHMM_glimmerT_19905-T1
Valid prediction for GlimmerHMM_glimmerT_19897-T1
Valid prediction for snap_scaffold_8-snap.609-T1
Valid prediction for GlimmerHMM_glimmerT_19906-T1
Valid prediction for snap_scaffold_8-snap.631-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 GlimmerHMM_glimmerT_19900-T1
Valid prediction for GlimmerHMM_glimmerT_19887-T1
Valid prediction for GeneMark_model.33998_t
Valid prediction for GeneMark_model.34023_t
Valid prediction for GeneMark_model.34020_t
Valid prediction for GeneMark_model.34022_t
Valid prediction for snap_scaffold_8-snap.636-T1
Valid prediction for GlimmerHMM_glimmerT_19894-T1
Valid prediction for GeneMark_model.34012_t
Valid prediction for GeneMark_model.34018_t
Valid prediction for GeneMark_model.34029_t
Valid prediction for snap_scaffold_8-snap.619-T1
Valid prediction for GeneMark_model.34010_t
Valid prediction for GeneMark_model.34015_t
Valid prediction for GeneMark_model.34034_t
Valid prediction for GeneMark_model.34024_t
Valid prediction for GeneMark_model.33996_t
Valid prediction for GeneMark_model.34026_t
Valid prediction for snap_scaffold_8-snap.608-T1
Valid prediction for snap_scaffold_8-snap.630-T1
Valid prediction for GlimmerHMM_glimmerT_19902-T1
Valid prediction for GeneMark_model.34000_t
Valid prediction for snap_scaffold_8-snap.640-T1
Valid prediction for snap_scaffold_8-snap.626-T1
Valid prediction for GlimmerHMM_glimmerT_19896-T1
Valid prediction for Augustus_model.g13303.t1
Valid prediction for GeneMark_model.34030_t
Valid prediction for GeneMark_model.34009_t
Valid prediction for GlimmerHMM_glimmerT_19904-T1
Valid prediction for snap_scaffold_8-snap.624-T1
Valid prediction for snap_scaffold_8-snap.611-T1
Valid prediction for snap_scaffold_8-snap.613-T1
Valid prediction for snap_scaffold_8-snap.625-T1
Valid prediction for GlimmerHMM_glimmerT_19889-T1
Valid prediction for snap_scaffold_8-snap.639-T1
Valid prediction for GeneMark_model.34002_t
Valid prediction for snap_scaffold_8-snap.632-T1
Valid prediction for snap_scaffold_8-snap.628-T1
Valid prediction for GeneMark_model.33999_t
Valid prediction for GeneMark_model.34017_t
Valid prediction for snap_scaffold_8-snap.627-T1
Valid prediction for Augustus_model.g13300.t1
Valid prediction for GlimmerHMM_glimmerT_19903-T1
Valid prediction for GeneMark_model.34004_t
Valid prediction for snap_scaffold_8-snap.617-T1
Valid prediction for Augustus_model.g13298.t1
Valid prediction for GlimmerHMM_glimmerT_19901-T1
Valid prediction for snap_scaffold_8-snap.620-T1
Valid prediction for snap_scaffold_8-snap.614-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.612-T1
Valid prediction for snap_scaffold_8-snap.622-T1
Valid prediction for GlimmerHMM_glimmerT_19890-T1
Valid prediction for GeneMark_model.34032_t
Valid prediction for GlimmerHMM_glimmerT_19893-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16549, rend_intergenic: 7190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39577, rend_intergenic: 21381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80363, rend_intergenic: 75728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87892, rend_intergenic: 82708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102399, rend_intergenic: 98704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128881, rend_intergenic: 120676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135551, rend_intergenic: 133690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155230, rend_intergenic: 151258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176036, rend_intergenic: 165757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178013
-exon list size: 503


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
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1.4    
1.6    
1.8    
2.0    
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2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
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4.2    
4.4    
4.6    
4.8    
5.0    
5.1    
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5.5    
5.7    
5.9    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.3    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
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17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 16549, rend_intergenic: 7190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39577, rend_intergenic: 21381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80363, rend_intergenic: 75728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87892, rend_intergenic: 82708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102399, rend_intergenic: 98704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128881, rend_intergenic: 120676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135551, rend_intergenic: 133690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155230, rend_intergenic: 151258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176036, rend_intergenic: 165757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 8 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21761
-exon list size: 42


building trellis

2.3    
4.5    
6.8    
9.1    
11.4    
13.6    
15.9    
18.2    
20.5    
22.7    
25.0    
27.3    
29.5    
31.8    
34.1    
36.4    
38.6    
40.9    
43.2    
45.5    
47.7    
50.0    
52.3    
54.5    
56.8    
59.1    
61.4    
63.6    
65.9    
68.2    
70.5    
72.7    
75.0    
77.3    
79.5    
81.8    
84.1    
86.4    
88.6    
90.9    
93.2    
95.5    
97.7    
-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 1 - 13206
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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