-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_10623149-10758828

-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 HiQ_model.g29683.t1
Valid prediction for GlimmerHMM_glimmerT_44783-T1
Valid prediction for snap_scaffold_19-snap.2023-T1
Valid prediction for snap_scaffold_19-snap.2026-T1
Valid prediction for snap_scaffold_19-snap.2052-T1
Valid prediction for GlimmerHMM_glimmerT_44781-T1
Valid prediction for pasa_asmbl_21648.p1
Valid prediction for snap_scaffold_19-snap.2053-T1
Valid prediction for snap_scaffold_19-snap.2040-T1
Valid prediction for Augustus_model.g29700.t1
Valid prediction for Augustus_model.g29697.t1
Valid prediction for Augustus_model.g29692.t1
Valid prediction for snap_scaffold_19-snap.2043-T1
Valid prediction for Augustus_model.g29695.t1
Valid prediction for snap_scaffold_19-snap.2057-T1
Valid prediction for CodingQuarry_transcript_25784-T1
Valid prediction for snap_scaffold_19-snap.2036-T1
Valid prediction for Augustus_model.g29687.t1
Valid prediction for GlimmerHMM_glimmerT_44777-T1
Valid prediction for snap_scaffold_19-snap.2038-T1
Valid prediction for GlimmerHMM_glimmerT_44788-T1
Valid prediction for snap_scaffold_19-snap.2051-T1
Valid prediction for snap_scaffold_19-snap.2029-T1
Valid prediction for snap_scaffold_19-snap.2055-T1
Valid prediction for Augustus_model.g29696.t1
Valid prediction for Augustus_model.g29684.t1
Valid prediction for Augustus_model.g29690.t1
Valid prediction for snap_scaffold_19-snap.2042-T1
Valid prediction for GlimmerHMM_glimmerT_44792-T1
Valid prediction for snap_scaffold_19-snap.2034-T1
Valid prediction for GlimmerHMM_glimmerT_44769-T1
Valid prediction for GlimmerHMM_glimmerT_44786-T1
Valid prediction for snap_scaffold_19-snap.2019-T1
Valid prediction for snap_scaffold_19-snap.2018-T1
Valid prediction for GlimmerHMM_glimmerT_44765-T1
Valid prediction for Augustus_model.g29686.t1
Valid prediction for GlimmerHMM_glimmerT_44766-T1
Valid prediction for snap_scaffold_19-snap.2037-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.2032-T1
Valid prediction for snap_scaffold_19-snap.2047-T1
Valid prediction for snap_scaffold_19-snap.2045-T1
Valid prediction for snap_scaffold_19-snap.2025-T1
Valid prediction for Augustus_model.g29694.t1
Valid prediction for GlimmerHMM_glimmerT_44785-T1
Valid prediction for GlimmerHMM_glimmerT_44782-T1
Valid prediction for GlimmerHMM_glimmerT_44768-T1
Valid prediction for GlimmerHMM_glimmerT_44791-T1
Valid prediction for GlimmerHMM_glimmerT_44787-T1
Valid prediction for GlimmerHMM_glimmerT_44789-T1
Valid prediction for GlimmerHMM_glimmerT_44773-T1
Valid prediction for Augustus_model.g29698.t1
Valid prediction for snap_scaffold_19-snap.2049-T1
Valid prediction for GlimmerHMM_glimmerT_44790-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_19-snap.2044-T1
Valid prediction for snap_scaffold_19-snap.2027-T1
Valid prediction for snap_scaffold_19-snap.2054-T1
Valid prediction for GlimmerHMM_glimmerT_44774-T1
Valid prediction for snap_scaffold_19-snap.2030-T1
Valid prediction for snap_scaffold_19-snap.2024-T1
Valid prediction for snap_scaffold_19-snap.2035-T1
Valid prediction for GlimmerHMM_glimmerT_44776-T1
Valid prediction for Augustus_model.g29689.t1
Valid prediction for Augustus_model.g29685.t1
Valid prediction for GlimmerHMM_glimmerT_44775-T1
Valid prediction for snap_scaffold_19-snap.2046-T1
Valid prediction for snap_scaffold_19-snap.2028-T1
Valid prediction for GlimmerHMM_glimmerT_44784-T1
Valid prediction for snap_scaffold_19-snap.2021-T1
Valid prediction for GlimmerHMM_glimmerT_44770-T1
Valid prediction for GlimmerHMM_glimmerT_44779-T1
Valid prediction for GlimmerHMM_glimmerT_44780-T1
Valid prediction for Augustus_model.g29688.t1
Valid prediction for snap_scaffold_19-snap.2039-T1
Valid prediction for snap_scaffold_19-snap.2041-T1
Valid prediction for CodingQuarry_transcript_25785-T1
Valid prediction for GlimmerHMM_glimmerT_44772-T1
Couldn't classify 121357, 121401
Sorry, prediction pasa_asmbl_22350.p1 fails validation.
(TCC)	 CC	121357-121401	GT	TGG
(GTG)	 AG	121506-121589	GT	AGG
(GTT)	 AG	121688-121829	GT	AGG
(ACG)	 AG	121930-122033	CC	GAC
-recovered pasa_asmbl_22350.p1, terminal, 121930, 122033
-recovered pasa_asmbl_22350.p1, internal, 121506, 121589
-recovered pasa_asmbl_22350.p1, internal, 121688, 121829
Valid prediction for GlimmerHMM_glimmerT_44778-T1
Valid prediction for Augustus_model.g29691.t1
Valid prediction for GlimmerHMM_glimmerT_44771-T1
Valid prediction for snap_scaffold_19-snap.2031-T1
Valid prediction for snap_scaffold_19-snap.2056-T1
Valid prediction for GlimmerHMM_glimmerT_44767-T1
Valid prediction for snap_scaffold_19-snap.2020-T1
Valid prediction for Augustus_model.g29699.t1
Valid prediction for Augustus_model.g29693.t1
Valid prediction for snap_scaffold_19-snap.2022-T1
Valid prediction for snap_scaffold_19-snap.2033-T1
Valid prediction for snap_scaffold_19-snap.2050-T1
Valid prediction for snap_scaffold_19-snap.2048-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12772, rend_intergenic: 6605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21011, rend_intergenic: 17822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21317, rend_intergenic: 21107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25104, rend_intergenic: 21526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32006, rend_intergenic: 27025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47991, rend_intergenic: 43479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56873, rend_intergenic: 49644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73770, rend_intergenic: 58643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81228, rend_intergenic: 76793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87517, rend_intergenic: 84619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90802, rend_intergenic: 89186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97731, rend_intergenic: 93977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100249, rend_intergenic: 98320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101406, rend_intergenic: 101014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106493, rend_intergenic: 102811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123768, rend_intergenic: 111884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128777, rend_intergenic: 125722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 135680
-exon list size: 350


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 12772, rend_intergenic: 6605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21011, rend_intergenic: 17822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21317, rend_intergenic: 21107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25104, rend_intergenic: 21526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32006, rend_intergenic: 27025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47991, rend_intergenic: 43479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56873, rend_intergenic: 49644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73770, rend_intergenic: 58643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81228, rend_intergenic: 76793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87517, rend_intergenic: 84619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90802, rend_intergenic: 89186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97731, rend_intergenic: 93977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100249, rend_intergenic: 98320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101406, rend_intergenic: 101014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106493, rend_intergenic: 102811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123768, rend_intergenic: 111884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128777, rend_intergenic: 125722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support