-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_16843349-17095359

-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_28574-T1
Valid prediction for snap_scaffold_11-snap.3444-T1
Valid prediction for snap_scaffold_11-snap.3472-T1
Valid prediction for Augustus_model.g18916.t1
Valid prediction for GlimmerHMM_glimmerT_28586-T1
Valid prediction for GlimmerHMM_glimmerT_28566-T1
Valid prediction for snap_scaffold_11-snap.3456-T1
Valid prediction for Augustus_model.g18920.t1
Valid prediction for GlimmerHMM_glimmerT_28564-T1
Valid prediction for Augustus_model.g18926.t1
Valid prediction for snap_scaffold_11-snap.3483-T1
Valid prediction for CodingQuarry_transcript_8353-T1
Valid prediction for snap_scaffold_11-snap.3440-T1
Valid prediction for snap_scaffold_11-snap.3438-T1
Valid prediction for snap_scaffold_11-snap.3445-T1
Valid prediction for GlimmerHMM_glimmerT_28573-T1
Valid prediction for snap_scaffold_11-snap.3452-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_28589-T1
Valid prediction for Augustus_model.g18915.t1
Valid prediction for Augustus_model.g18913.t1
Valid prediction for GlimmerHMM_glimmerT_28563-T1
Valid prediction for GlimmerHMM_glimmerT_28593-T1
Valid prediction for GlimmerHMM_glimmerT_28584-T1
Valid prediction for GlimmerHMM_glimmerT_28567-T1
Valid prediction for snap_scaffold_11-snap.3455-T1
Valid prediction for snap_scaffold_11-snap.3449-T1
Valid prediction for Augustus_model.g18914.t1
Valid prediction for snap_scaffold_11-snap.3459-T1
Valid prediction for GlimmerHMM_glimmerT_28558-T1
Valid prediction for Augustus_model.g18909.t1
Valid prediction for pasa_asmbl_6187.p1
Valid prediction for GlimmerHMM_glimmerT_28587-T1
Valid prediction for snap_scaffold_11-snap.3480-T1
Valid prediction for GlimmerHMM_glimmerT_28577-T1
Valid prediction for snap_scaffold_11-snap.3446-T1
Valid prediction for Augustus_model.g18922.t1
Valid prediction for GlimmerHMM_glimmerT_28582-T1
Valid prediction for snap_scaffold_11-snap.3460-T1
Valid prediction for Augustus_model.g18925.t1
Valid prediction for snap_scaffold_11-snap.3470-T1
Valid prediction for GlimmerHMM_glimmerT_28571-T1
Valid prediction for GlimmerHMM_glimmerT_28570-T1
Valid prediction for GlimmerHMM_glimmerT_28580-T1
Valid prediction for GlimmerHMM_glimmerT_28565-T1
Valid prediction for snap_scaffold_11-snap.3473-T1
Valid prediction for Augustus_model.g18912.t1
Valid prediction for GlimmerHMM_glimmerT_28581-T1
Valid prediction for snap_scaffold_11-snap.3484-T1
Valid prediction for GlimmerHMM_glimmerT_28588-T1
Couldn't classify 112471, 112688
Sorry, prediction pasa_asmbl_6181.p1 fails validation.
(ATG)	 AG	110709-110853	GT	AGG
(GTT)	 AG	112471-112688	TA	AGT
-recovered pasa_asmbl_6181.p1, initial, 110709, 110853
-recovered pasa_asmbl_6181.p1, internal, 110709, 110853
Valid prediction for snap_scaffold_11-snap.3466-T1
Valid prediction for GlimmerHMM_glimmerT_28576-T1
Valid prediction for Augustus_model.g18924.t1
Valid prediction for snap_scaffold_11-snap.3441-T1
Valid prediction for snap_scaffold_11-snap.3464-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_28572-T1
Valid prediction for GlimmerHMM_glimmerT_28556-T1
Valid prediction for GlimmerHMM_glimmerT_28560-T1
Valid prediction for GlimmerHMM_glimmerT_28575-T1
Valid prediction for GlimmerHMM_glimmerT_28569-T1
Valid prediction for CodingQuarry_transcript_8356-T1
Couldn't classify 24936, 25059
Sorry, prediction pasa_asmbl_7242.p1 fails validation.
(CGC)	 AC	24936-25059	GT	GGG
(GAA)	 AG	25280-25381	GT	TGG
(AGA)	 AG	25528-25670	GT	AGG
(CTG)	 AG	25944-25991	TG	GAT
-recovered pasa_asmbl_7242.p1, terminal, 25944, 25991
-recovered pasa_asmbl_7242.p1, internal, 25280, 25381
-recovered pasa_asmbl_7242.p1, internal, 25528, 25670
Valid prediction for snap_scaffold_11-snap.3454-T1
Valid prediction for snap_scaffold_11-snap.3433-T1
Valid prediction for CodingQuarry_transcript_8355-T1
Valid prediction for snap_scaffold_11-snap.3458-T1
Valid prediction for snap_scaffold_11-snap.3443-T1
Valid prediction for snap_scaffold_11-snap.3474-T1
Valid prediction for snap_scaffold_11-snap.3436-T1
Valid prediction for snap_scaffold_11-snap.3450-T1
Valid prediction for Augustus_model.g18910.t1
Valid prediction for snap_scaffold_11-snap.3465-T1
Valid prediction for snap_scaffold_11-snap.3442-T1
Valid prediction for CodingQuarry_transcript_8354-T1
Valid prediction for snap_scaffold_11-snap.3481-T1
Valid prediction for GlimmerHMM_glimmerT_28561-T1
Valid prediction for Augustus_model.g18921.t1
Valid prediction for snap_scaffold_11-snap.3482-T1
Valid prediction for snap_scaffold_11-snap.3475-T1
Valid prediction for Augustus_model.g18918.t1
Valid prediction for GlimmerHMM_glimmerT_28592-T1
Valid prediction for snap_scaffold_11-snap.3462-T1
Valid prediction for snap_scaffold_11-snap.3437-T1
Valid prediction for GlimmerHMM_glimmerT_28579-T1
Valid prediction for GlimmerHMM_glimmerT_28591-T1
Valid prediction for snap_scaffold_11-snap.3471-T1
Valid prediction for GlimmerHMM_glimmerT_28590-T1
Couldn't classify 191899, 192249
Sorry, prediction pasa_asmbl_6179.p1 fails validation.
(CTT)	 CT	191899-192249	TT	AGT
Valid prediction for snap_scaffold_11-snap.3478-T1
Valid prediction for snap_scaffold_11-snap.3435-T1
Valid prediction for GlimmerHMM_glimmerT_28583-T1
Valid prediction for Augustus_model.g18919.t1
Valid prediction for snap_scaffold_11-snap.3463-T1
Valid prediction for snap_scaffold_11-snap.3461-T1
Valid prediction for snap_scaffold_11-snap.3485-T1
Valid prediction for GlimmerHMM_glimmerT_28585-T1
Valid prediction for GlimmerHMM_glimmerT_28578-T1
Valid prediction for CodingQuarry_transcript_8357-T1
Valid prediction for GlimmerHMM_glimmerT_28594-T1
Valid prediction for GlimmerHMM_glimmerT_28559-T1
Valid prediction for snap_scaffold_11-snap.3457-T1
Valid prediction for snap_scaffold_11-snap.3447-T1
Valid prediction for snap_scaffold_11-snap.3434-T1
Valid prediction for Augustus_model.g18917.t1
Valid prediction for HiQ_model.g18930.t1
Valid prediction for Augustus_model.g18911.t1
Valid prediction for snap_scaffold_11-snap.3453-T1
Valid prediction for GlimmerHMM_glimmerT_28562-T1
Valid prediction for Augustus_model.g18923.t1
Valid prediction for snap_scaffold_11-snap.3439-T1
Valid prediction for snap_scaffold_11-snap.3468-T1
Valid prediction for Augustus_model.g18928.t1
Valid prediction for GlimmerHMM_glimmerT_28557-T1
Valid prediction for GlimmerHMM_glimmerT_28568-T1
Valid prediction for snap_scaffold_11-snap.3451-T1
Valid prediction for snap_scaffold_11-snap.3479-T1
Valid prediction for snap_scaffold_11-snap.3467-T1
Valid prediction for snap_scaffold_11-snap.3448-T1
Valid prediction for Augustus_model.g18929.t1
Valid prediction for snap_scaffold_11-snap.3469-T1
Valid prediction for snap_scaffold_11-snap.3477-T1
Valid prediction for Augustus_model.g18908.t1
Valid prediction for Augustus_model.g18927.t1
Valid prediction for snap_scaffold_11-snap.3476-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24203, rend_intergenic: 20360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37502, rend_intergenic: 25589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48784, rend_intergenic: 42219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55806, rend_intergenic: 51671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76893, rend_intergenic: 56080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98371, rend_intergenic: 83333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99880, rend_intergenic: 98474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108658, rend_intergenic: 100870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117558, rend_intergenic: 112854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131582, rend_intergenic: 118709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154058, rend_intergenic: 132529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156364, rend_intergenic: 155802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159621, rend_intergenic: 158267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160582, rend_intergenic: 159720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172731, rend_intergenic: 160689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200454, rend_intergenic: 194690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202494, rend_intergenic: 200579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208685, rend_intergenic: 205786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223063, rend_intergenic: 209192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231250, rend_intergenic: 229090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236140, rend_intergenic: 231602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244858, rend_intergenic: 240636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249140, rend_intergenic: 246553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 252011
-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 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 24203, rend_intergenic: 20360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37502, rend_intergenic: 25589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48784, rend_intergenic: 42219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55806, rend_intergenic: 51671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76893, rend_intergenic: 56080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98371, rend_intergenic: 83333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99880, rend_intergenic: 98474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108658, rend_intergenic: 100870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117558, rend_intergenic: 112854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131582, rend_intergenic: 118709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154058, rend_intergenic: 132529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156364, rend_intergenic: 155802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159621, rend_intergenic: 158267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160582, rend_intergenic: 159720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172731, rend_intergenic: 160689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200454, rend_intergenic: 194690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202494, rend_intergenic: 200579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208685, rend_intergenic: 205786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223063, rend_intergenic: 209192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231250, rend_intergenic: 229090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236140, rend_intergenic: 231602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244858, rend_intergenic: 240636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249140, rend_intergenic: 246553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support