-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_1-179548

-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_1-snap.34-T1
Valid prediction for snap_scaffold_1-snap.20-T1
Valid prediction for snap_scaffold_1-snap.24-T1
Valid prediction for snap_scaffold_1-snap.16-T1
Valid prediction for snap_scaffold_1-snap.36-T1
Valid prediction for Augustus_model.g13.t1
Valid prediction for GlimmerHMM_glimmerT_20-T1
Valid prediction for GlimmerHMM_glimmerT_2-T1
Valid prediction for CodingQuarry_transcript_2502-T1
Valid prediction for HiQ_model.g15.t1
Valid prediction for GlimmerHMM_glimmerT_17-T1
Valid prediction for snap_scaffold_1-snap.21-T1
Valid prediction for pasa_asmbl_1388.p1
Valid prediction for HiQ_model.g2.t1
Valid prediction for snap_scaffold_1-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_1-T1
Valid prediction for snap_scaffold_1-snap.22-T1
Valid prediction for Augustus_model.g7.t1
Valid prediction for snap_scaffold_1-snap.32-T1
Couldn't classify 94419, 94571
Sorry, prediction pasa_asmbl_2796.p1 fails validation.
(GAT)	 CA	94419-94571	GT	AGG
(GGG)	 AG	94815-94953	GT	CGG
(CTA)	 AG	95447-95670	GT	ATG
(CCC)	 AG	96310-96516	GT	AGG
(GTG)	 AG	96888-97131	GT	AGG
(ACC)	 AG	97397-97644	CT	GAC
-recovered pasa_asmbl_2796.p1, terminal, 97397, 97644
-recovered pasa_asmbl_2796.p1, internal, 94815, 94953
-recovered pasa_asmbl_2796.p1, internal, 95447, 95670
-recovered pasa_asmbl_2796.p1, internal, 96310, 96516
-recovered pasa_asmbl_2796.p1, internal, 96888, 97131
Valid prediction for pasa_asmbl_1400.p1
Valid prediction for pasa_asmbl_1395.p1
Valid prediction for snap_scaffold_1-snap.18-T1
Valid prediction for Augustus_model.g8.t1
Valid prediction for snap_scaffold_1-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_13-T1
Valid prediction for GlimmerHMM_glimmerT_19-T1
Valid prediction for snap_scaffold_1-snap.23-T1
Valid prediction for snap_scaffold_1-snap.12-T1
Valid prediction for snap_scaffold_1-snap.25-T1
Valid prediction for snap_scaffold_1-snap.27-T1
Valid prediction for Augustus_model.g9.t1
Valid prediction for Augustus_model.g14.t1
Valid prediction for GlimmerHMM_glimmerT_15-T1
Valid prediction for HiQ_model.g10.t1
Valid prediction for snap_scaffold_1-snap.26-T1
Valid prediction for GlimmerHMM_glimmerT_11-T1
Valid prediction for snap_scaffold_1-snap.28-T1
Valid prediction for GlimmerHMM_glimmerT_18-T1
Valid prediction for GlimmerHMM_glimmerT_14-T1
Valid prediction for snap_scaffold_1-snap.35-T1
Valid prediction for Augustus_model.g1.t1
add_exon() Sorry, Augustus_model.g1.t1 1-220-initial-1 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 365-532-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 883-1150-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 1397-1512-internal-3 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 2256-2372-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 3988-4204-internal-3 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 4333-6109-internal-1 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 6268-6435-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 6818-6985-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 8399-8532-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 8817-8961-internal-1 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 9816-9986-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 11363-11533-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 12790-12948-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 16078-16613-terminal-1 is invalid.
Valid prediction for Augustus_model.g12.t1
Valid prediction for snap_scaffold_1-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_7-T1
Valid prediction for snap_scaffold_1-snap.1-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_12-T1
Valid prediction for CodingQuarry_transcript_2503-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_1-snap.10-T1
Valid prediction for snap_scaffold_1-snap.37-T1
Valid prediction for pasa_asmbl_2.p1
Valid prediction for GlimmerHMM_glimmerT_5-T1
Valid prediction for snap_scaffold_1-snap.14-T1
Valid prediction for Augustus_model.g3.t1
Valid prediction for GlimmerHMM_glimmerT_10-T1
Valid prediction for snap_scaffold_1-snap.7-T1
Valid prediction for snap_scaffold_1-snap.29-T1
Valid prediction for GlimmerHMM_glimmerT_9-T1
Valid prediction for snap_scaffold_1-snap.11-T1
Valid prediction for snap_scaffold_1-snap.9-T1
Valid prediction for snap_scaffold_1-snap.31-T1
Valid prediction for GlimmerHMM_glimmerT_6-T1
Valid prediction for Augustus_model.g11.t1
Valid prediction for snap_scaffold_1-snap.30-T1
Valid prediction for GlimmerHMM_glimmerT_3-T1
Valid prediction for snap_scaffold_1-snap.8-T1
Valid prediction for HiQ_model.g5.t1
Valid prediction for pasa_asmbl_1.p1
Valid prediction for snap_scaffold_1-snap.17-T1
Valid prediction for snap_scaffold_1-snap.5-T1
Valid prediction for snap_scaffold_1-snap.19-T1
Valid prediction for GlimmerHMM_glimmerT_4-T1
Valid prediction for snap_scaffold_1-snap.15-T1
Valid prediction for Augustus_model.g6.t1
Valid prediction for snap_scaffold_1-snap.6-T1
Valid prediction for HiQ_model.g16.t1
Valid prediction for Augustus_model.g4.t1
Valid prediction for GlimmerHMM_glimmerT_16-T1
Valid prediction for snap_scaffold_1-snap.13-T1
Valid prediction for pasa_asmbl_15.p1
Valid prediction for GlimmerHMM_glimmerT_8-T1
Couldn't classify 90668, 91075
Sorry, prediction pasa_asmbl_1394.p3 fails validation.
(GTG)	 CT	90668-91075	CC	AAC
Valid prediction for GlimmerHMM_glimmerT_21-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 55618, rend_intergenic: 55166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59180, rend_intergenic: 55771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76004, rend_intergenic: 74672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78265, rend_intergenic: 76156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88803, rend_intergenic: 86092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148723, rend_intergenic: 140087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179548
-exon list size: 369


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.0    
21.3    
21.6    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.5    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.5    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 55618, rend_intergenic: 55166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59180, rend_intergenic: 55771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76004, rend_intergenic: 74672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78265, rend_intergenic: 76156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88803, rend_intergenic: 86092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148723, rend_intergenic: 140087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support