-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_2721846-2871152

-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.632-T1
Valid prediction for Augustus_model.g4041.t1
Valid prediction for snap_scaffold_3-snap.647-T1
Valid prediction for Augustus_model.g4038.t1
Valid prediction for snap_scaffold_3-snap.631-T1
Valid prediction for snap_scaffold_3-snap.640-T1
Valid prediction for snap_scaffold_3-snap.635-T1
Valid prediction for snap_scaffold_3-snap.643-T1
Valid prediction for GlimmerHMM_glimmerT_6207-T1
Valid prediction for snap_scaffold_3-snap.650-T1
Valid prediction for snap_scaffold_3-snap.641-T1
Valid prediction for snap_scaffold_3-snap.623-T1
Valid prediction for snap_scaffold_3-snap.622-T1
Valid prediction for GlimmerHMM_glimmerT_6202-T1
Valid prediction for GlimmerHMM_glimmerT_6221-T1
Valid prediction for snap_scaffold_3-snap.634-T1
Valid prediction for GlimmerHMM_glimmerT_6219-T1
Valid prediction for GlimmerHMM_glimmerT_6215-T1
Valid prediction for snap_scaffold_3-snap.626-T1
Valid prediction for Augustus_model.g4042.t1
Valid prediction for GlimmerHMM_glimmerT_6217-T1
Valid prediction for snap_scaffold_3-snap.646-T1
Valid prediction for snap_scaffold_3-snap.642-T1
Valid prediction for GlimmerHMM_glimmerT_6218-T1
Couldn't classify 114775, 114993
Sorry, prediction pasa_asmbl_39920.p1 fails validation.
(GAT)	 CA	114775-114993	GT	TTG
(GGT)	 AG	115158-115277	GT	AGG
(TGC)	 AG	115576-115707	AG	GAA
-recovered pasa_asmbl_39920.p1, terminal, 115576, 115707
-recovered pasa_asmbl_39920.p1, internal, 115158, 115277
Valid prediction for snap_scaffold_3-snap.630-T1
Valid prediction for snap_scaffold_3-snap.627-T1
Valid prediction for snap_scaffold_3-snap.624-T1
Valid prediction for snap_scaffold_3-snap.645-T1
Valid prediction for GlimmerHMM_glimmerT_6208-T1
Valid prediction for GlimmerHMM_glimmerT_6204-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_6223-T1
Valid prediction for Augustus_model.g4044.t1
Valid prediction for snap_scaffold_3-snap.636-T1
Valid prediction for snap_scaffold_3-snap.638-T1
Valid prediction for GlimmerHMM_glimmerT_6213-T1
Valid prediction for snap_scaffold_3-snap.628-T1
Valid prediction for snap_scaffold_3-snap.639-T1
Valid prediction for Augustus_model.g4040.t1
Valid prediction for snap_scaffold_3-snap.633-T1
Valid prediction for snap_scaffold_3-snap.649-T1
Valid prediction for Augustus_model.g4045.t1
Valid prediction for GlimmerHMM_glimmerT_6210-T1
Valid prediction for GlimmerHMM_glimmerT_6211-T1
Valid prediction for GlimmerHMM_glimmerT_6220-T1
Valid prediction for GlimmerHMM_glimmerT_6222-T1
Valid prediction for snap_scaffold_3-snap.637-T1
Valid prediction for GlimmerHMM_glimmerT_6214-T1
Valid prediction for snap_scaffold_3-snap.629-T1
Valid prediction for GlimmerHMM_glimmerT_6216-T1
Valid prediction for Augustus_model.g4039.t1
Valid prediction for GlimmerHMM_glimmerT_6206-T1
Valid prediction for GlimmerHMM_glimmerT_6203-T1
Valid prediction for GlimmerHMM_glimmerT_6205-T1
Valid prediction for GlimmerHMM_glimmerT_6212-T1
Valid prediction for GlimmerHMM_glimmerT_6209-T1
Valid prediction for Augustus_model.g4043.t1
Valid prediction for snap_scaffold_3-snap.648-T1
Valid prediction for snap_scaffold_3-snap.644-T1
Valid prediction for snap_scaffold_3-snap.625-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34270, rend_intergenic: 29518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40856, rend_intergenic: 39367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50248, rend_intergenic: 44117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62351, rend_intergenic: 60720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139014, rend_intergenic: 120631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140704, rend_intergenic: 139339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 149307
-exon list size: 178


building trellis

0.6    
1.1    
1.7    
2.2    
2.8    
3.3    
3.9    
4.4    
5.0    
5.6    
6.1    
6.7    
7.2    
7.8    
8.3    
8.9    
9.4    
10.0    
10.6    
11.1    
11.7    
12.2    
12.8    
13.3    
13.9    
14.4    
15.0    
15.6    
16.1    
16.7    
17.2    
17.8    
18.3    
18.9    
19.4    
20.0    
20.6    
21.1    
21.7    
22.2    
22.8    
23.3    
23.9    
24.4    
25.0    
25.6    
26.1    
26.7    
27.2    
27.8    
28.3    
28.9    
29.4    
30.0    
30.6    
31.1    
31.7    
32.2    
32.8    
33.3    
33.9    
34.4    
35.0    
35.6    
36.1    
36.7    
37.2    
37.8    
38.3    
38.9    
39.4    
40.0    
40.6    
41.1    
41.7    
42.2    
42.8    
43.3    
43.9    
44.4    
45.0    
45.6    
46.1    
46.7    
47.2    
47.8    
48.3    
48.9    
49.4    
50.0    
50.6    
51.1    
51.7    
52.2    
52.8    
53.3    
53.9    
54.4    
55.0    
55.6    
56.1    
56.7    
57.2    
57.8    
58.3    
58.9    
59.4    
60.0    
60.6    
61.1    
61.7    
62.2    
62.8    
63.3    
63.9    
64.4    
65.0    
65.6    
66.1    
66.7    
67.2    
67.8    
68.3    
68.9    
69.4    
70.0    
70.6    
71.1    
71.7    
72.2    
72.8    
73.3    
73.9    
74.4    
75.0    
75.6    
76.1    
76.7    
77.2    
77.8    
78.3    
78.9    
79.4    
80.0    
80.6    
81.1    
81.7    
82.2    
82.8    
83.3    
83.9    
84.4    
85.0    
85.6    
86.1    
86.7    
87.2    
87.8    
88.3    
88.9    
89.4    
90.0    
90.6    
91.1    
91.7    
92.2    
92.8    
93.3    
93.9    
94.4    
95.0    
95.6    
96.1    
96.7    
97.2    
97.8    
98.3    
98.9    
99.4    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 34270, rend_intergenic: 29518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40856, rend_intergenic: 39367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50248, rend_intergenic: 44117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62351, rend_intergenic: 60720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139014, rend_intergenic: 120631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140704, rend_intergenic: 139339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support