-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_1934612-2145385

-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 snap_scaffold_3-snap.475-T1
Valid prediction for snap_scaffold_3-snap.469-T1
Valid prediction for snap_scaffold_3-snap.489-T1
Valid prediction for GlimmerHMM_glimmerT_6106-T1
Valid prediction for GlimmerHMM_glimmerT_6108-T1
Valid prediction for snap_scaffold_3-snap.480-T1
Valid prediction for snap_scaffold_3-snap.472-T1
Valid prediction for snap_scaffold_3-snap.493-T1
Valid prediction for snap_scaffold_3-snap.466-T1
Valid prediction for Augustus_model.g3993.t1
Valid prediction for snap_scaffold_3-snap.481-T1
Valid prediction for GlimmerHMM_glimmerT_6100-T1
Valid prediction for snap_scaffold_3-snap.484-T1
Valid prediction for snap_scaffold_3-snap.488-T1
Valid prediction for Augustus_model.g3991.t1
Valid prediction for snap_scaffold_3-snap.486-T1
Valid prediction for GlimmerHMM_glimmerT_6102-T1
Valid prediction for snap_scaffold_3-snap.476-T1
Valid prediction for Augustus_model.g3988.t1
Valid prediction for snap_scaffold_3-snap.479-T1
Valid prediction for snap_scaffold_3-snap.499-T1
Valid prediction for snap_scaffold_3-snap.464-T1
Valid prediction for snap_scaffold_3-snap.496-T1
Valid prediction for snap_scaffold_3-snap.485-T1
Couldn't classify 14370, 14513
Sorry, prediction pasa_asmbl_40827.p2 fails validation.
(ATG)	 GG	11442-11516	GT	AGG
(TGG)	 AG	12511-12621	GT	TGG
(ACA)	 AG	12828-12923	GT	AGG
(GCA)	 AG	14101-14208	GT	TGG
(GCA)	 AG	14370-14513	GT	AGG
-recovered pasa_asmbl_40827.p2, initial, 11442, 11516
-recovered pasa_asmbl_40827.p2, internal, 12511, 12621
-recovered pasa_asmbl_40827.p2, internal, 12828, 12923
-recovered pasa_asmbl_40827.p2, internal, 14101, 14208
-recovered pasa_asmbl_40827.p2, internal, 14370, 14513
Valid prediction for Augustus_model.g3985.t1
Valid prediction for GlimmerHMM_glimmerT_6110-T1
Valid prediction for GlimmerHMM_glimmerT_6115-T1
Valid prediction for GlimmerHMM_glimmerT_6117-T1
Valid prediction for GlimmerHMM_glimmerT_6112-T1
Couldn't classify 16915, 17007
Couldn't classify 17976, 18059
Sorry, prediction pasa_asmbl_40828.p1 fails validation.
(TTT)	 AG	16915-17007	GT	AGG
(AAC)	 AG	17451-17576	GT	AGG
(CCT)	 AG	17976-18059	GT	CCG
-recovered pasa_asmbl_40828.p1, internal, 16915, 17007
-recovered pasa_asmbl_40828.p1, internal, 17451, 17576
-recovered pasa_asmbl_40828.p1, internal, 17976, 18059
Valid prediction for Augustus_model.g3981.t1
Valid prediction for snap_scaffold_3-snap.490-T1
Valid prediction for snap_scaffold_3-snap.465-T1
Valid prediction for snap_scaffold_3-snap.468-T1
Valid prediction for snap_scaffold_3-snap.495-T1
Valid prediction for Augustus_model.g3987.t1
Valid prediction for Augustus_model.g3982.t1
Valid prediction for GlimmerHMM_glimmerT_6101-T1
Valid prediction for GlimmerHMM_glimmerT_6114-T1
Valid prediction for Augustus_model.g3990.t1
Valid prediction for GlimmerHMM_glimmerT_6109-T1
Valid prediction for GlimmerHMM_glimmerT_6119-T1
Valid prediction for GlimmerHMM_glimmerT_6103-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 snap_scaffold_3-snap.494-T1
Valid prediction for Augustus_model.g3994.t1
Valid prediction for GlimmerHMM_glimmerT_6107-T1
Valid prediction for Augustus_model.g3992.t1
Valid prediction for Augustus_model.g3983.t1
Valid prediction for GlimmerHMM_glimmerT_6122-T1
Valid prediction for Augustus_model.g3995.t1
Valid prediction for snap_scaffold_3-snap.482-T1
Valid prediction for GlimmerHMM_glimmerT_6118-T1
Valid prediction for GlimmerHMM_glimmerT_6104-T1
Valid prediction for GlimmerHMM_glimmerT_6099-T1
Valid prediction for snap_scaffold_3-snap.487-T1
Valid prediction for GlimmerHMM_glimmerT_6116-T1
Valid prediction for snap_scaffold_3-snap.473-T1
Valid prediction for snap_scaffold_3-snap.470-T1
Valid prediction for snap_scaffold_3-snap.467-T1
Valid prediction for snap_scaffold_3-snap.478-T1
Valid prediction for GlimmerHMM_glimmerT_6113-T1
Valid prediction for snap_scaffold_3-snap.500-T1
Valid prediction for snap_scaffold_3-snap.491-T1
Valid prediction for snap_scaffold_3-snap.474-T1
Valid prediction for Augustus_model.g3984.t1
Valid prediction for GlimmerHMM_glimmerT_6105-T1
Valid prediction for snap_scaffold_3-snap.471-T1
Valid prediction for snap_scaffold_3-snap.492-T1
Valid prediction for snap_scaffold_3-snap.483-T1
Valid prediction for snap_scaffold_3-snap.498-T1
Valid prediction for GlimmerHMM_glimmerT_6121-T1
Valid prediction for Augustus_model.g3989.t1
Valid prediction for GlimmerHMM_glimmerT_6120-T1
Valid prediction for Augustus_model.g3986.t1
Valid prediction for snap_scaffold_3-snap.497-T1
Valid prediction for GlimmerHMM_glimmerT_6111-T1
Valid prediction for snap_scaffold_3-snap.477-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 65466, rend_intergenic: 61602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68235, rend_intergenic: 67062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85715, rend_intergenic: 77229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93773, rend_intergenic: 89070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114624, rend_intergenic: 108884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121674, rend_intergenic: 118325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143330, rend_intergenic: 139822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171658, rend_intergenic: 168044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210774
-exon list size: 253


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.7    
3.1    
3.5    
3.9    
4.3    
4.7    
5.1    
5.5    
5.9    
6.3    
6.7    
7.1    
7.5    
7.8    
8.2    
8.6    
9.0    
9.4    
9.8    
10.2    
10.6    
11.0    
11.4    
11.8    
12.2    
12.5    
12.9    
13.3    
13.7    
14.1    
14.5    
14.9    
15.3    
15.7    
16.1    
16.5    
16.9    
17.3    
17.6    
18.0    
18.4    
18.8    
19.2    
19.6    
20.0    
20.4    
20.8    
21.2    
21.6    
22.0    
22.4    
22.7    
23.1    
23.5    
23.9    
24.3    
24.7    
25.1    
25.5    
25.9    
26.3    
26.7    
27.1    
27.5    
27.8    
28.2    
28.6    
29.0    
29.4    
29.8    
30.2    
30.6    
31.0    
31.4    
31.8    
32.2    
32.5    
32.9    
33.3    
33.7    
34.1    
34.5    
34.9    
35.3    
35.7    
36.1    
36.5    
36.9    
37.3    
37.6    
38.0    
38.4    
38.8    
39.2    
39.6    
40.0    
40.4    
40.8    
41.2    
41.6    
42.0    
42.4    
42.7    
43.1    
43.5    
43.9    
44.3    
44.7    
45.1    
45.5    
45.9    
46.3    
46.7    
47.1    
47.5    
47.8    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.2    
52.5    
52.9    
53.3    
53.7    
54.1    
54.5    
54.9    
55.3    
55.7    
56.1    
56.5    
56.9    
57.3    
57.6    
58.0    
58.4    
58.8    
59.2    
59.6    
60.0    
60.4    
60.8    
61.2    
61.6    
62.0    
62.4    
62.7    
63.1    
63.5    
63.9    
64.3    
64.7    
65.1    
65.5    
65.9    
66.3    
66.7    
67.1    
67.5    
67.8    
68.2    
68.6    
69.0    
69.4    
69.8    
70.2    
70.6    
71.0    
71.4    
71.8    
72.2    
72.5    
72.9    
73.3    
73.7    
74.1    
74.5    
74.9    
75.3    
75.7    
76.1    
76.5    
76.9    
77.3    
77.6    
78.0    
78.4    
78.8    
79.2    
79.6    
80.0    
80.4    
80.8    
81.2    
81.6    
82.0    
82.4    
82.7    
83.1    
83.5    
83.9    
84.3    
84.7    
85.1    
85.5    
85.9    
86.3    
86.7    
87.1    
87.5    
87.8    
88.2    
88.6    
89.0    
89.4    
89.8    
90.2    
90.6    
91.0    
91.4    
91.8    
92.2    
92.5    
92.9    
93.3    
93.7    
94.1    
94.5    
94.9    
95.3    
95.7    
96.1    
96.5    
96.9    
97.3    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 65466, rend_intergenic: 61602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68235, rend_intergenic: 67062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85715, rend_intergenic: 77229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93773, rend_intergenic: 89070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114624, rend_intergenic: 108884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121674, rend_intergenic: 118325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143330, rend_intergenic: 139822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171658, rend_intergenic: 168044  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