-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_4898222-5050847

-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 GlimmerHMM_glimmerT_43265-T1
Valid prediction for GlimmerHMM_glimmerT_43252-T1
Valid prediction for GeneMark_model.74687_t
Valid prediction for GlimmerHMM_glimmerT_43268-T1
Valid prediction for GlimmerHMM_glimmerT_43250-T1
Valid prediction for GlimmerHMM_glimmerT_43264-T1
Valid prediction for Augustus_model.g28946.t1
Valid prediction for snap_scaffold_18-snap.1025-T1
Valid prediction for GeneMark_model.74678_t
Valid prediction for snap_scaffold_18-snap.1011-T1
Valid prediction for GeneMark_model.74683_t
Valid prediction for GeneMark_model.74664_t
Valid prediction for snap_scaffold_18-snap.1017-T1
Valid prediction for GlimmerHMM_glimmerT_43260-T1
Valid prediction for snap_scaffold_18-snap.1010-T1
Valid prediction for GeneMark_model.74690_t
Valid prediction for snap_scaffold_18-snap.1027-T1
Valid prediction for GeneMark_model.74666_t
Valid prediction for snap_scaffold_18-snap.1018-T1
Valid prediction for Augustus_model.g28941.t1
Valid prediction for HiQ_model.g28940.t1
Valid prediction for GeneMark_model.74685_t
Valid prediction for CodingQuarry_transcript_23709-T1
Valid prediction for GlimmerHMM_glimmerT_43253-T1
Valid prediction for snap_scaffold_18-snap.1005-T1
Valid prediction for Augustus_model.g28939.t1
Valid prediction for snap_scaffold_18-snap.1006-T1
Valid prediction for snap_scaffold_18-snap.999-T1
Valid prediction for snap_scaffold_18-snap.1016-T1
Valid prediction for GlimmerHMM_glimmerT_43274-T1
Valid prediction for GlimmerHMM_glimmerT_43273-T1
Valid prediction for GeneMark_model.74698_t
Valid prediction for Augustus_model.g28933.t1
Valid prediction for snap_scaffold_18-snap.1001-T1
Valid prediction for snap_scaffold_18-snap.994-T1
Valid prediction for GeneMark_model.74670_t
Valid prediction for Augustus_model.g28931.t1
Valid prediction for GeneMark_model.74681_t
Valid prediction for GeneMark_model.74695_t
Valid prediction for snap_scaffold_18-snap.1026-T1
Valid prediction for pasa_asmbl_20605.p1
Valid prediction for GlimmerHMM_glimmerT_43266-T1
Valid prediction for GeneMark_model.74674_t
Valid prediction for snap_scaffold_18-snap.995-T1
Valid prediction for GeneMark_model.74696_t
Valid prediction for Augustus_model.g28934.t1
Valid prediction for GeneMark_model.74672_t
Valid prediction for snap_scaffold_18-snap.1008-T1
Valid prediction for GeneMark_model.74691_t
Valid prediction for snap_scaffold_18-snap.996-T1
Valid prediction for snap_scaffold_18-snap.1021-T1
Valid prediction for GeneMark_model.74668_t
Valid prediction for GlimmerHMM_glimmerT_43258-T1
Valid prediction for snap_scaffold_18-snap.1013-T1
Valid prediction for GlimmerHMM_glimmerT_43263-T1
Valid prediction for Augustus_model.g28936.t1
Valid prediction for Augustus_model.g28942.t1
Valid prediction for GlimmerHMM_glimmerT_43256-T1
Valid prediction for snap_scaffold_18-snap.1019-T1
Valid prediction for GlimmerHMM_glimmerT_43248-T1
Valid prediction for GeneMark_model.74676_t
Valid prediction for snap_scaffold_18-snap.1004-T1
Valid prediction for GeneMark_model.74692_t
Valid prediction for Augustus_model.g28947.t1
Valid prediction for Augustus_model.g28948.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 GeneMark_model.74669_t
Valid prediction for GeneMark_model.74680_t
Valid prediction for snap_scaffold_18-snap.1007-T1
Valid prediction for GeneMark_model.74684_t
Valid prediction for GlimmerHMM_glimmerT_43254-T1
Couldn't classify 26621, 26846
Sorry, prediction pasa_asmbl_19865.p1 fails validation.
(AGG)	 CC	26621-26846	GT	GGG
(CGG)	 AG	27434-27657	GT	AGG
(GCC)	 AG	27863-28077	GT	AAG
(GTC)	 AG	28383-28493	GT	GGG
(GAG)	 AG	28799-28943	GT	GGG
(AGC)	 AG	29115-29327	CA	AGC
-recovered pasa_asmbl_19865.p1, terminal, 29115, 29327
-recovered pasa_asmbl_19865.p1, internal, 27434, 27657
-recovered pasa_asmbl_19865.p1, internal, 27863, 28077
-recovered pasa_asmbl_19865.p1, internal, 28383, 28493
-recovered pasa_asmbl_19865.p1, internal, 28799, 28943
Valid prediction for Augustus_model.g28938.t1
Valid prediction for snap_scaffold_18-snap.1000-T1
Valid prediction for GlimmerHMM_glimmerT_43259-T1
Valid prediction for HiQ_model.g28945.t1
Valid prediction for GeneMark_model.74682_t
Valid prediction for snap_scaffold_18-snap.1022-T1
Couldn't classify 50576, 50600
Sorry, prediction GeneMark_model.74689_t fails validation.
(ATG)	 AG	49256-49273	GT	AGG
(ATC)	 AG	49377-49468	GT	AGG
(GGA)	 AG	50576-50600	GT	CTG
-recovered GeneMark_model.74689_t, initial, 49256, 49273
-recovered GeneMark_model.74689_t, internal, 49256, 49273
-recovered GeneMark_model.74689_t, internal, 49377, 49468
-recovered GeneMark_model.74689_t, internal, 50576, 50600
Valid prediction for GlimmerHMM_glimmerT_43270-T1
Valid prediction for Augustus_model.g28943.t1
Valid prediction for GlimmerHMM_glimmerT_43267-T1
Valid prediction for GlimmerHMM_glimmerT_43262-T1
Valid prediction for snap_scaffold_18-snap.998-T1
Valid prediction for Augustus_model.g28944.t1
Valid prediction for GeneMark_model.74675_t
Valid prediction for GeneMark_model.74671_t
Valid prediction for snap_scaffold_18-snap.1020-T1
Valid prediction for GlimmerHMM_glimmerT_43249-T1
Valid prediction for snap_scaffold_18-snap.1024-T1
Valid prediction for GeneMark_model.74679_t
Valid prediction for snap_scaffold_18-snap.1012-T1
Valid prediction for Augustus_model.g28937.t1
Valid prediction for GeneMark_model.74677_t
Valid prediction for GlimmerHMM_glimmerT_43255-T1
Valid prediction for GeneMark_model.74694_t
Valid prediction for GeneMark_model.74693_t
Valid prediction for GeneMark_model.74697_t
Valid prediction for snap_scaffold_18-snap.1023-T1
Valid prediction for GlimmerHMM_glimmerT_43272-T1
Valid prediction for snap_scaffold_18-snap.1002-T1
Valid prediction for snap_scaffold_18-snap.1003-T1
Valid prediction for GlimmerHMM_glimmerT_43257-T1
Valid prediction for GeneMark_model.74686_t
Valid prediction for snap_scaffold_18-snap.1009-T1
Valid prediction for GlimmerHMM_glimmerT_43269-T1
Valid prediction for GeneMark_model.74665_t
Valid prediction for GlimmerHMM_glimmerT_43251-T1
Valid prediction for GeneMark_model.74663_t
Valid prediction for Augustus_model.g28935.t1
Valid prediction for snap_scaffold_18-snap.1014-T1
Valid prediction for snap_scaffold_18-snap.1015-T1
Valid prediction for GlimmerHMM_glimmerT_43271-T1
Valid prediction for Augustus_model.g28932.t1
Valid prediction for GeneMark_model.74673_t
Valid prediction for GeneMark_model.74688_t
Valid prediction for GeneMark_model.74667_t
Valid prediction for snap_scaffold_18-snap.997-T1
Valid prediction for GlimmerHMM_glimmerT_43261-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39044, rend_intergenic: 35451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46518, rend_intergenic: 41065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81722, rend_intergenic: 78976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89477, rend_intergenic: 86578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 152626
-exon list size: 416


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.2    
2.4    
2.6    
2.9    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.5    
4.8    
5.0    
5.3    
5.5    
5.7    
6.0    
6.2    
6.5    
6.7    
6.9    
7.2    
7.4    
7.7    
7.9    
8.1    
8.4    
8.6    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
10.3    
10.5    
10.8    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.6    
13.9    
14.1    
14.4    
14.6    
14.8    
15.1    
15.3    
15.6    
15.8    
16.0    
16.3    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
17.9    
18.2    
18.4    
18.7    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.5    
21.8    
22.0    
22.2    
22.5    
22.7    
23.0    
23.2    
23.4    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.0    
27.3    
27.5    
27.8    
28.0    
28.2    
28.5    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
67.9    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.5    
71.8    
72.0    
72.2    
72.5    
72.7    
73.0    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 39044, rend_intergenic: 35451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46518, rend_intergenic: 41065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81722, rend_intergenic: 78976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89477, rend_intergenic: 86578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19210
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-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 5771 - 19210
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-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 5983 - 19210
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-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 5983 - 16164
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

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