-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_496337-662201

-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.129-T1
Valid prediction for pasa_asmbl_39812.p1
Valid prediction for snap_scaffold_3-snap.161-T1
Valid prediction for snap_scaffold_3-snap.170-T1
Valid prediction for snap_scaffold_3-snap.146-T1
Valid prediction for snap_scaffold_3-snap.168-T1
Valid prediction for GlimmerHMM_glimmerT_5905-T1
Valid prediction for GlimmerHMM_glimmerT_5894-T1
Valid prediction for GlimmerHMM_glimmerT_5901-T1
Valid prediction for GlimmerHMM_glimmerT_5895-T1
Valid prediction for snap_scaffold_3-snap.138-T1
Valid prediction for snap_scaffold_3-snap.148-T1
Valid prediction for Augustus_model.g3852.t1
Valid prediction for GlimmerHMM_glimmerT_5897-T1
Valid prediction for snap_scaffold_3-snap.119-T1
Valid prediction for snap_scaffold_3-snap.132-T1
Valid prediction for snap_scaffold_3-snap.140-T1
Valid prediction for Augustus_model.g3849.t1
Valid prediction for GlimmerHMM_glimmerT_5891-T1
Valid prediction for snap_scaffold_3-snap.156-T1
Valid prediction for snap_scaffold_3-snap.126-T1
Valid prediction for snap_scaffold_3-snap.164-T1
Valid prediction for snap_scaffold_3-snap.158-T1
Valid prediction for snap_scaffold_3-snap.123-T1
Valid prediction for CodingQuarry_transcript_46063-T1
Valid prediction for HiQ_model.g3850.t1
Valid prediction for GlimmerHMM_glimmerT_5890-T1
Valid prediction for GlimmerHMM_glimmerT_5904-T1
Valid prediction for snap_scaffold_3-snap.169-T1
Valid prediction for snap_scaffold_3-snap.141-T1
Valid prediction for snap_scaffold_3-snap.137-T1
Valid prediction for GlimmerHMM_glimmerT_5899-T1
Valid prediction for snap_scaffold_3-snap.135-T1
Valid prediction for GlimmerHMM_glimmerT_5906-T1
Valid prediction for snap_scaffold_3-snap.121-T1
Valid prediction for snap_scaffold_3-snap.125-T1
Valid prediction for Augustus_model.g3851.t1
Valid prediction for snap_scaffold_3-snap.120-T1
Valid prediction for CodingQuarry_transcript_46064-T1
Valid prediction for Augustus_model.g3848.t1
Valid prediction for snap_scaffold_3-snap.151-T1
Valid prediction for snap_scaffold_3-snap.133-T1
Valid prediction for snap_scaffold_3-snap.142-T1
Valid prediction for snap_scaffold_3-snap.150-T1
Valid prediction for snap_scaffold_3-snap.128-T1
Valid prediction for snap_scaffold_3-snap.165-T1
Valid prediction for snap_scaffold_3-snap.149-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.127-T1
Valid prediction for snap_scaffold_3-snap.154-T1
Valid prediction for GlimmerHMM_glimmerT_5892-T1
Valid prediction for snap_scaffold_3-snap.157-T1
Valid prediction for snap_scaffold_3-snap.139-T1
Valid prediction for Augustus_model.g3857.t1
Valid prediction for GlimmerHMM_glimmerT_5907-T1
Valid prediction for Augustus_model.g3854.t1
Valid prediction for GlimmerHMM_glimmerT_5893-T1
Valid prediction for snap_scaffold_3-snap.144-T1
Valid prediction for Augustus_model.g3859.t1
Valid prediction for Augustus_model.g3853.t1
Valid prediction for snap_scaffold_3-snap.167-T1
Valid prediction for HiQ_model.g3855.t1
Valid prediction for snap_scaffold_3-snap.166-T1
Valid prediction for GlimmerHMM_glimmerT_5912-T1
Valid prediction for snap_scaffold_3-snap.159-T1
Couldn't classify 55076, 55281
Sorry, prediction pasa_asmbl_38667.p1 fails validation.
(TTC)	 TG	55076-55281	GT	AGG
(TGT)	 AG	55841-56180	GA	GAG
-recovered pasa_asmbl_38667.p1, terminal, 55841, 56180
Valid prediction for snap_scaffold_3-snap.147-T1
Valid prediction for snap_scaffold_3-snap.160-T1
Valid prediction for Augustus_model.g3856.t1
Valid prediction for snap_scaffold_3-snap.130-T1
Valid prediction for GlimmerHMM_glimmerT_5898-T1
Valid prediction for snap_scaffold_3-snap.124-T1
Valid prediction for GlimmerHMM_glimmerT_5909-T1
Valid prediction for snap_scaffold_3-snap.134-T1
Valid prediction for Augustus_model.g3846.t1
Valid prediction for GlimmerHMM_glimmerT_5902-T1
Valid prediction for GlimmerHMM_glimmerT_5911-T1
Valid prediction for Augustus_model.g3847.t1
Valid prediction for snap_scaffold_3-snap.163-T1
Valid prediction for snap_scaffold_3-snap.131-T1
Valid prediction for snap_scaffold_3-snap.143-T1
Valid prediction for snap_scaffold_3-snap.155-T1
Valid prediction for GlimmerHMM_glimmerT_5900-T1
Valid prediction for GlimmerHMM_glimmerT_5889-T1
Valid prediction for GlimmerHMM_glimmerT_5908-T1
Valid prediction for snap_scaffold_3-snap.153-T1
Valid prediction for snap_scaffold_3-snap.122-T1
Valid prediction for GlimmerHMM_glimmerT_5913-T1
Valid prediction for GlimmerHMM_glimmerT_5903-T1
Valid prediction for snap_scaffold_3-snap.162-T1
Valid prediction for snap_scaffold_3-snap.145-T1
Valid prediction for Augustus_model.g3858.t1
Valid prediction for snap_scaffold_3-snap.136-T1
Valid prediction for GlimmerHMM_glimmerT_5910-T1
Valid prediction for GlimmerHMM_glimmerT_5896-T1
Valid prediction for pasa_asmbl_38669.p1
Valid prediction for snap_scaffold_3-snap.152-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17606, rend_intergenic: 14188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22565, rend_intergenic: 20170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26962, rend_intergenic: 25245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30981, rend_intergenic: 27332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37888, rend_intergenic: 34697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48948, rend_intergenic: 47126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65149, rend_intergenic: 62013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80164, rend_intergenic: 72310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91288, rend_intergenic: 84768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94173, rend_intergenic: 92856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99263, rend_intergenic: 96916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122188, rend_intergenic: 120653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124176, rend_intergenic: 122634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131103, rend_intergenic: 129172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135257, rend_intergenic: 132755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146482, rend_intergenic: 142452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148689, rend_intergenic: 147659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160661, rend_intergenic: 152915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165865
-exon list size: 321


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 17606, rend_intergenic: 14188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22565, rend_intergenic: 20170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26962, rend_intergenic: 25245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30981, rend_intergenic: 27332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37888, rend_intergenic: 34697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48948, rend_intergenic: 47126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65149, rend_intergenic: 62013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80164, rend_intergenic: 72310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91288, rend_intergenic: 84768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94173, rend_intergenic: 92856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99263, rend_intergenic: 96916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122188, rend_intergenic: 120653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124176, rend_intergenic: 122634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131103, rend_intergenic: 129172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135257, rend_intergenic: 132755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146482, rend_intergenic: 142452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148689, rend_intergenic: 147659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160661, rend_intergenic: 152915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support