-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_12102860-12393583

-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_7453-T1
Valid prediction for snap_scaffold_3-snap.2402-T1
Valid prediction for GlimmerHMM_glimmerT_7435-T1
Couldn't classify 105158, 106174
Sorry, prediction pasa_asmbl_40396.p1 fails validation.
(ATG)	 GC	105158-106174	TG	GGT
Valid prediction for snap_scaffold_3-snap.2379-T1
Valid prediction for snap_scaffold_3-snap.2401-T1
Valid prediction for GlimmerHMM_glimmerT_7432-T1
Valid prediction for GlimmerHMM_glimmerT_7440-T1
Valid prediction for GlimmerHMM_glimmerT_7445-T1
Valid prediction for Augustus_model.g4851.t1
Valid prediction for snap_scaffold_3-snap.2399-T1
Valid prediction for GlimmerHMM_glimmerT_7437-T1
Valid prediction for snap_scaffold_3-snap.2409-T1
Valid prediction for snap_scaffold_3-snap.2396-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g4848.t1
Valid prediction for snap_scaffold_3-snap.2410-T1
Valid prediction for snap_scaffold_3-snap.2405-T1
Valid prediction for snap_scaffold_3-snap.2407-T1
Valid prediction for snap_scaffold_3-snap.2408-T1
Valid prediction for snap_scaffold_3-snap.2404-T1
Valid prediction for snap_scaffold_3-snap.2384-T1
Valid prediction for Augustus_model.g4843.t1
Valid prediction for snap_scaffold_3-snap.2393-T1
Valid prediction for snap_scaffold_3-snap.2387-T1
Valid prediction for GlimmerHMM_glimmerT_7448-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.2382-T1
Valid prediction for snap_scaffold_3-snap.2398-T1
Valid prediction for snap_scaffold_3-snap.2400-T1
Valid prediction for snap_scaffold_3-snap.2391-T1
Valid prediction for Augustus_model.g4844.t1
Valid prediction for snap_scaffold_3-snap.2380-T1
Valid prediction for GlimmerHMM_glimmerT_7434-T1
Valid prediction for snap_scaffold_3-snap.2383-T1
Valid prediction for GlimmerHMM_glimmerT_7441-T1
Valid prediction for snap_scaffold_3-snap.2390-T1
Valid prediction for CodingQuarry_transcript_46295-T1
Valid prediction for snap_scaffold_3-snap.2406-T1
Valid prediction for GlimmerHMM_glimmerT_7447-T1
Valid prediction for GlimmerHMM_glimmerT_7433-T1
Valid prediction for snap_scaffold_3-snap.2403-T1
Valid prediction for snap_scaffold_3-snap.2386-T1
Valid prediction for snap_scaffold_3-snap.2388-T1
Valid prediction for snap_scaffold_3-snap.2394-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g4846.t1
Valid prediction for GlimmerHMM_glimmerT_7451-T1
Valid prediction for GlimmerHMM_glimmerT_7454-T1
Valid prediction for GlimmerHMM_glimmerT_7439-T1
Valid prediction for snap_scaffold_3-snap.2378-T1
Valid prediction for GlimmerHMM_glimmerT_7442-T1
Valid prediction for Augustus_model.g4849.t1
Valid prediction for GlimmerHMM_glimmerT_7443-T1
Valid prediction for GlimmerHMM_glimmerT_7446-T1
Valid prediction for snap_scaffold_3-snap.2381-T1
Couldn't classify 248289, 249026
Sorry, prediction pasa_asmbl_39206.p1 fails validation.
(GTT)	 AG	248289-249026	AA	GCA
Valid prediction for snap_scaffold_3-snap.2392-T1
Valid prediction for Augustus_model.g4840.t1
Valid prediction for snap_scaffold_3-snap.2385-T1
Valid prediction for pasa_asmbl_39205.p1
Valid prediction for GlimmerHMM_glimmerT_7449-T1
Valid prediction for GlimmerHMM_glimmerT_7444-T1
Valid prediction for Augustus_model.g4841.t1
Valid prediction for Augustus_model.g4850.t1
Valid prediction for snap_scaffold_3-snap.2389-T1
Valid prediction for GlimmerHMM_glimmerT_7452-T1
Valid prediction for GlimmerHMM_glimmerT_7436-T1
Valid prediction for Augustus_model.g4845.t1
Valid prediction for snap_scaffold_3-snap.2397-T1
Valid prediction for Augustus_model.g4847.t1
Valid prediction for GlimmerHMM_glimmerT_7438-T1
Valid prediction for snap_scaffold_3-snap.2395-T1
Valid prediction for Augustus_model.g4852.t1
Valid prediction for GlimmerHMM_glimmerT_7450-T1
Valid prediction for Augustus_model.g4839.t1
Valid prediction for Augustus_model.g4842.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15938, rend_intergenic: 12977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110022, rend_intergenic: 107337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 264469, rend_intergenic: 263821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 290724
-exon list size: 225


building trellis

0.4    
0.9    
1.3    
1.8    
2.2    
2.6    
3.1    
3.5    
4.0    
4.4    
4.8    
5.3    
5.7    
6.2    
6.6    
7.0    
7.5    
7.9    
8.4    
8.8    
9.3    
9.7    
10.1    
10.6    
11.0    
11.5    
11.9    
12.3    
12.8    
13.2    
13.7    
14.1    
14.5    
15.0    
15.4    
15.9    
16.3    
16.7    
17.2    
17.6    
18.1    
18.5    
18.9    
19.4    
19.8    
20.3    
20.7    
21.1    
21.6    
22.0    
22.5    
22.9    
23.3    
23.8    
24.2    
24.7    
25.1    
25.6    
26.0    
26.4    
26.9    
27.3    
27.8    
28.2    
28.6    
29.1    
29.5    
30.0    
30.4    
30.8    
31.3    
31.7    
32.2    
32.6    
33.0    
33.5    
33.9    
34.4    
34.8    
35.2    
35.7    
36.1    
36.6    
37.0    
37.4    
37.9    
38.3    
38.8    
39.2    
39.6    
40.1    
40.5    
41.0    
41.4    
41.9    
42.3    
42.7    
43.2    
43.6    
44.1    
44.5    
44.9    
45.4    
45.8    
46.3    
46.7    
47.1    
47.6    
48.0    
48.5    
48.9    
49.3    
49.8    
50.2    
50.7    
51.1    
51.5    
52.0    
52.4    
52.9    
53.3    
53.7    
54.2    
54.6    
55.1    
55.5    
55.9    
56.4    
56.8    
57.3    
57.7    
58.1    
58.6    
59.0    
59.5    
59.9    
60.4    
60.8    
61.2    
61.7    
62.1    
62.6    
63.0    
63.4    
63.9    
64.3    
64.8    
65.2    
65.6    
66.1    
66.5    
67.0    
67.4    
67.8    
68.3    
68.7    
69.2    
69.6    
70.0    
70.5    
70.9    
71.4    
71.8    
72.2    
72.7    
73.1    
73.6    
74.0    
74.4    
74.9    
75.3    
75.8    
76.2    
76.7    
77.1    
77.5    
78.0    
78.4    
78.9    
79.3    
79.7    
80.2    
80.6    
81.1    
81.5    
81.9    
82.4    
82.8    
83.3    
83.7    
84.1    
84.6    
85.0    
85.5    
85.9    
86.3    
86.8    
87.2    
87.7    
88.1    
88.5    
89.0    
89.4    
89.9    
90.3    
90.7    
91.2    
91.6    
92.1    
92.5    
93.0    
93.4    
93.8    
94.3    
94.7    
95.2    
95.6    
96.0    
96.5    
96.9    
97.4    
97.8    
98.2    
98.7    
99.1    
99.6    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 15938, rend_intergenic: 12977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110022, rend_intergenic: 107337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 264469, rend_intergenic: 263821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12976
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 12826
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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