-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_17517737-17726004

-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 Augustus_model.g9005.t1
Valid prediction for snap_scaffold_5-snap.3270-T1
Valid prediction for snap_scaffold_5-snap.3273-T1
Valid prediction for snap_scaffold_5-snap.3287-T1
Valid prediction for snap_scaffold_5-snap.3291-T1
Valid prediction for Augustus_model.g8998.t1
Valid prediction for GlimmerHMM_glimmerT_13537-T1
Valid prediction for snap_scaffold_5-snap.3289-T1
Valid prediction for Augustus_model.g9000.t1
Valid prediction for GlimmerHMM_glimmerT_13565-T1
Valid prediction for Augustus_model.g9004.t1
Valid prediction for snap_scaffold_5-snap.3258-T1
Valid prediction for GlimmerHMM_glimmerT_13550-T1
Valid prediction for snap_scaffold_5-snap.3259-T1
Valid prediction for Augustus_model.g8992.t1
Valid prediction for GlimmerHMM_glimmerT_13554-T1
Valid prediction for Augustus_model.g8995.t1
Valid prediction for snap_scaffold_5-snap.3269-T1
Valid prediction for GlimmerHMM_glimmerT_13548-T1
Valid prediction for GlimmerHMM_glimmerT_13543-T1
Valid prediction for Augustus_model.g9001.t1
Valid prediction for Augustus_model.g8997.t1
Valid prediction for Augustus_model.g9002.t1
Valid prediction for snap_scaffold_5-snap.3290-T1
Valid prediction for snap_scaffold_5-snap.3278-T1
Valid prediction for GlimmerHMM_glimmerT_13542-T1
Valid prediction for snap_scaffold_5-snap.3260-T1
Valid prediction for GlimmerHMM_glimmerT_13557-T1
Valid prediction for GlimmerHMM_glimmerT_13539-T1
Valid prediction for snap_scaffold_5-snap.3266-T1
Valid prediction for snap_scaffold_5-snap.3276-T1
Valid prediction for snap_scaffold_5-snap.3264-T1
Valid prediction for GlimmerHMM_glimmerT_13551-T1
Valid prediction for Augustus_model.g8990.t1
Valid prediction for snap_scaffold_5-snap.3267-T1
Valid prediction for snap_scaffold_5-snap.3282-T1
Valid prediction for GlimmerHMM_glimmerT_13552-T1
Valid prediction for snap_scaffold_5-snap.3281-T1
Valid prediction for GlimmerHMM_glimmerT_13541-T1
Valid prediction for GlimmerHMM_glimmerT_13549-T1
Valid prediction for Augustus_model.g9007.t1
Valid prediction for GlimmerHMM_glimmerT_13533-T1
Valid prediction for snap_scaffold_5-snap.3279-T1
Valid prediction for snap_scaffold_5-snap.3262-T1
Valid prediction for GlimmerHMM_glimmerT_13544-T1
Valid prediction for GlimmerHMM_glimmerT_13559-T1
Valid prediction for snap_scaffold_5-snap.3286-T1
Valid prediction for GlimmerHMM_glimmerT_13546-T1
Valid prediction for snap_scaffold_5-snap.3284-T1
Valid prediction for GlimmerHMM_glimmerT_13561-T1
Couldn't classify 92527, 93519
Sorry, prediction pasa_asmbl_46182.p1 fails validation.
(ACC)	 AC	92527-93519	TT	TGT
Valid prediction for GlimmerHMM_glimmerT_13538-T1
Valid prediction for Augustus_model.g8991.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_13555-T1
Valid prediction for Augustus_model.g8999.t1
Valid prediction for GlimmerHMM_glimmerT_13560-T1
Valid prediction for snap_scaffold_5-snap.3275-T1
Valid prediction for snap_scaffold_5-snap.3293-T1
Valid prediction for snap_scaffold_5-snap.3265-T1
Valid prediction for snap_scaffold_5-snap.3261-T1
Couldn't classify 56047, 56154
Sorry, prediction pasa_asmbl_44807.p1 fails validation.
(ATG)	 AA	53882-54018	GT	ACG
(GTT)	 AG	54486-54636	GT	AGG
(GTG)	 AG	54723-54829	GT	AGG
(TCC)	 AG	55372-55486	GT	TGG
(GTG)	 AG	56047-56154	GT	TGG
-recovered pasa_asmbl_44807.p1, initial, 53882, 54018
-recovered pasa_asmbl_44807.p1, internal, 54486, 54636
-recovered pasa_asmbl_44807.p1, internal, 54723, 54829
-recovered pasa_asmbl_44807.p1, internal, 55372, 55486
-recovered pasa_asmbl_44807.p1, internal, 56047, 56154
Valid prediction for GlimmerHMM_glimmerT_13556-T1
Valid prediction for snap_scaffold_5-snap.3283-T1
Valid prediction for snap_scaffold_5-snap.3257-T1
Valid prediction for HiQ_model.g9003.t1
Valid prediction for GlimmerHMM_glimmerT_13534-T1
Valid prediction for GlimmerHMM_glimmerT_13563-T1
Valid prediction for GlimmerHMM_glimmerT_13545-T1
Valid prediction for Augustus_model.g9006.t1
Valid prediction for snap_scaffold_5-snap.3274-T1
Valid prediction for snap_scaffold_5-snap.3285-T1
Valid prediction for snap_scaffold_5-snap.3280-T1
Couldn't classify 5291, 5623
Sorry, prediction pasa_asmbl_44811.p1 fails validation.
(AGC)	 AA	5291-5623	GT	AGG
(CTC)	 AG	6089-6589	GC	AGG
-recovered pasa_asmbl_44811.p1, terminal, 6089, 6589
-recovered pasa_asmbl_44811.p1, internal, 6089, 6589
Valid prediction for snap_scaffold_5-snap.3271-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_13540-T1
Valid prediction for GlimmerHMM_glimmerT_13547-T1
Valid prediction for GlimmerHMM_glimmerT_13558-T1
Valid prediction for Augustus_model.g8993.t1
Valid prediction for GlimmerHMM_glimmerT_13566-T1
Valid prediction for GlimmerHMM_glimmerT_13562-T1
Valid prediction for GlimmerHMM_glimmerT_13553-T1
Valid prediction for snap_scaffold_5-snap.3277-T1
Valid prediction for GlimmerHMM_glimmerT_13536-T1
Valid prediction for Augustus_model.g8996.t1
Valid prediction for snap_scaffold_5-snap.3263-T1
Valid prediction for snap_scaffold_5-snap.3288-T1
Valid prediction for GlimmerHMM_glimmerT_13564-T1
Valid prediction for snap_scaffold_5-snap.3268-T1
Valid prediction for snap_scaffold_5-snap.3292-T1
Valid prediction for GlimmerHMM_glimmerT_13535-T1
Valid prediction for snap_scaffold_5-snap.3272-T1
Valid prediction for Augustus_model.g8994.t1
Valid prediction for Augustus_model.g9008.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26385, rend_intergenic: 9610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37814, rend_intergenic: 34883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42639, rend_intergenic: 41751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43700, rend_intergenic: 43100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46391, rend_intergenic: 44217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54128, rend_intergenic: 48900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78307, rend_intergenic: 63510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88174, rend_intergenic: 78624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113222, rend_intergenic: 109150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120315, rend_intergenic: 117828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122376, rend_intergenic: 120681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133285, rend_intergenic: 129911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138862, rend_intergenic: 133407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143395, rend_intergenic: 141839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149040, rend_intergenic: 145350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208268
-exon list size: 344


building trellis

0.3    
0.6    
0.9    
1.2    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.8    
99.1    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 26385, rend_intergenic: 9610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37814, rend_intergenic: 34883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42639, rend_intergenic: 41751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43700, rend_intergenic: 43100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46391, rend_intergenic: 44217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54128, rend_intergenic: 48900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78307, rend_intergenic: 63510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88174, rend_intergenic: 78624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113222, rend_intergenic: 109150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120315, rend_intergenic: 117828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122376, rend_intergenic: 120681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133285, rend_intergenic: 129911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138862, rend_intergenic: 133407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143395, rend_intergenic: 141839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149040, rend_intergenic: 145350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support