-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_1265623-1402301

-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.101006_t
Valid prediction for GlimmerHMM_glimmerT_58017-T1
Valid prediction for GlimmerHMM_glimmerT_58016-T1
Valid prediction for Augustus_model.g38653.t1
Valid prediction for snap_scaffold_27-snap.296-T1
Valid prediction for snap_scaffold_27-snap.294-T1
Valid prediction for Augustus_model.g38648.t1
Valid prediction for GlimmerHMM_glimmerT_58013-T1
Valid prediction for GlimmerHMM_glimmerT_58015-T1
Valid prediction for GlimmerHMM_glimmerT_58018-T1
Valid prediction for Augustus_model.g38651.t1
Valid prediction for GeneMark_model.100995_t
Valid prediction for GeneMark_model.100998_t
Valid prediction for snap_scaffold_27-snap.280-T1
Valid prediction for GeneMark_model.100990_t
Valid prediction for snap_scaffold_27-snap.288-T1
Couldn't classify 88406, 88508
Couldn't classify 88757, 88977
Sorry, prediction pasa_asmbl_36528.p2 fails validation.
(GGA)	 TG	88406-88508	GT	CAG
(TGG)	 AG	88757-88977	GC	CTG
-recovered pasa_asmbl_36528.p2, internal, 88757, 88977
Valid prediction for GlimmerHMM_glimmerT_58007-T1
Valid prediction for snap_scaffold_27-snap.292-T1
Valid prediction for GlimmerHMM_glimmerT_58008-T1
Valid prediction for snap_scaffold_27-snap.302-T1
Valid prediction for GeneMark_model.100994_t
Valid prediction for GeneMark_model.100997_t
Couldn't classify 118678, 119283
Sorry, prediction pasa_asmbl_36539.p1 fails validation.
(ATG)	 AG	118678-119283	AT	AGA
Valid prediction for Augustus_model.g38645.t1
Valid prediction for Augustus_model.g38647.t1
Valid prediction for GlimmerHMM_glimmerT_58014-T1
Valid prediction for snap_scaffold_27-snap.290-T1
Couldn't classify 96851, 97185
Sorry, prediction pasa_asmbl_36566.p1 fails validation.
(ATG)	 AC	95993-96014	GT	CAG
(ATG)	 AG	96851-97185	GG	GAG
-recovered pasa_asmbl_36566.p1, initial, 95993, 96014
Valid prediction for GlimmerHMM_glimmerT_58006-T1
Valid prediction for GeneMark_model.101009_t
Valid prediction for snap_scaffold_27-snap.301-T1
Valid prediction for GlimmerHMM_glimmerT_58012-T1
Valid prediction for Augustus_model.g38644.t1
Valid prediction for Augustus_model.g38650.t1
Couldn't classify 89047, 89895
Sorry, prediction pasa_asmbl_35959.p1 fails validation.
(TCC)	 TG	89047-89895	GA	AGG
Valid prediction for GeneMark_model.101004_t
Valid prediction for GeneMark_model.101008_t
Valid prediction for snap_scaffold_27-snap.299-T1
Valid prediction for snap_scaffold_27-snap.279-T1
Valid prediction for GeneMark_model.101002_t
Valid prediction for GlimmerHMM_glimmerT_58010-T1
Valid prediction for snap_scaffold_27-snap.282-T1
Valid prediction for Augustus_model.g38649.t1
Valid prediction for GeneMark_model.101005_t
Valid prediction for snap_scaffold_27-snap.297-T1
Valid prediction for snap_scaffold_27-snap.285-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_58005-T1
Valid prediction for snap_scaffold_27-snap.281-T1
Valid prediction for snap_scaffold_27-snap.287-T1
Valid prediction for snap_scaffold_27-snap.283-T1
Valid prediction for GeneMark_model.100992_t
Valid prediction for GeneMark_model.101003_t
Valid prediction for GeneMark_model.100999_t
Valid prediction for snap_scaffold_27-snap.286-T1
Valid prediction for GlimmerHMM_glimmerT_58009-T1
Valid prediction for GeneMark_model.101000_t
Valid prediction for GeneMark_model.101010_t
Valid prediction for Augustus_model.g38652.t1
Valid prediction for snap_scaffold_27-snap.291-T1
Valid prediction for snap_scaffold_27-snap.293-T1
Valid prediction for snap_scaffold_27-snap.295-T1
Valid prediction for Augustus_model.g38643.t1
Valid prediction for GeneMark_model.100996_t
Valid prediction for snap_scaffold_27-snap.284-T1
Valid prediction for GeneMark_model.101001_t
Couldn't classify 122974, 123025
Sorry, prediction pasa_asmbl_36701.p1 fails validation.
(CGC)	 AA	122974-123025	GT	AGG
(ATG)	 AG	123556-123645	GT	AGG
(GGT)	 AG	123861-123979	GT	CTG
(GTT)	 AG	124395-124509	GT	AGG
(TGG)	 AG	124629-124810	GT	GGG
(GTG)	 AG	125584-125811	GG	GAG
-recovered pasa_asmbl_36701.p1, initial, 123556, 123645
-recovered pasa_asmbl_36701.p1, terminal, 125584, 125811
-recovered pasa_asmbl_36701.p1, internal, 123556, 123645
-recovered pasa_asmbl_36701.p1, internal, 123861, 123979
-recovered pasa_asmbl_36701.p1, internal, 124395, 124509
-recovered pasa_asmbl_36701.p1, internal, 124629, 124810
Valid prediction for snap_scaffold_27-snap.289-T1
Valid prediction for snap_scaffold_27-snap.298-T1
Valid prediction for snap_scaffold_27-snap.303-T1
Valid prediction for GlimmerHMM_glimmerT_58011-T1
Valid prediction for GlimmerHMM_glimmerT_58003-T1
Valid prediction for GeneMark_model.100988_t
Valid prediction for GeneMark_model.101007_t
Valid prediction for snap_scaffold_27-snap.300-T1
Valid prediction for GeneMark_model.100991_t
Valid prediction for snap_scaffold_27-snap.304-T1
Valid prediction for Augustus_model.g38646.t1
Valid prediction for GeneMark_model.100989_t
Valid prediction for GlimmerHMM_glimmerT_58004-T1
Valid prediction for Augustus_model.g38642.t1
Valid prediction for Augustus_model.g38641.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18837, rend_intergenic: 10869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26272, rend_intergenic: 22653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31435, rend_intergenic: 27747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43031, rend_intergenic: 32467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70190, rend_intergenic: 67622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70992, rend_intergenic: 70702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78943, rend_intergenic: 71282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90312, rend_intergenic: 87868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108009, rend_intergenic: 105349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119721, rend_intergenic: 117744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 136679
-exon list size: 327


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 18837, rend_intergenic: 10869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26272, rend_intergenic: 22653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31435, rend_intergenic: 27747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43031, rend_intergenic: 32467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70190, rend_intergenic: 67622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70992, rend_intergenic: 70702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78943, rend_intergenic: 71282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90312, rend_intergenic: 87868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108009, rend_intergenic: 105349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119721, rend_intergenic: 117744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 122443 - 136679
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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 122443 - 134216
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal

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