-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_3973953-4160173

-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 pasa_asmbl_15119.p1
Valid prediction for snap_scaffold_15-snap.872-T1
Valid prediction for Augustus_model.g23974.t1
Valid prediction for snap_scaffold_15-snap.860-T1
Valid prediction for GlimmerHMM_glimmerT_35955-T1
Valid prediction for snap_scaffold_15-snap.861-T1
Valid prediction for snap_scaffold_15-snap.873-T1
Valid prediction for snap_scaffold_15-snap.854-T1
Valid prediction for snap_scaffold_15-snap.869-T1
Valid prediction for Augustus_model.g23978.t1
Valid prediction for snap_scaffold_15-snap.878-T1
Valid prediction for pasa_asmbl_15125.p1
Valid prediction for CodingQuarry_transcript_17966-T1
Valid prediction for snap_scaffold_15-snap.853-T1
Valid prediction for GlimmerHMM_glimmerT_35958-T1
Valid prediction for snap_scaffold_15-snap.883-T1
Valid prediction for snap_scaffold_15-snap.850-T1
Valid prediction for GlimmerHMM_glimmerT_35971-T1
Valid prediction for GlimmerHMM_glimmerT_35948-T1
Valid prediction for GlimmerHMM_glimmerT_35974-T1
Valid prediction for GlimmerHMM_glimmerT_35963-T1
Valid prediction for snap_scaffold_15-snap.870-T1
Valid prediction for GlimmerHMM_glimmerT_35961-T1
Valid prediction for snap_scaffold_15-snap.863-T1
Valid prediction for GlimmerHMM_glimmerT_35969-T1
Valid prediction for HiQ_model.g23985.t1
Valid prediction for GlimmerHMM_glimmerT_35951-T1
Valid prediction for snap_scaffold_15-snap.866-T1
Valid prediction for GlimmerHMM_glimmerT_35968-T1
Valid prediction for snap_scaffold_15-snap.885-T1
Valid prediction for snap_scaffold_15-snap.879-T1
Valid prediction for HiQ_model.g23984.t1
Valid prediction for Augustus_model.g23977.t1
Valid prediction for snap_scaffold_15-snap.852-T1
Valid prediction for Augustus_model.g23979.t1
Valid prediction for CodingQuarry_transcript_17967-T1
Valid prediction for Augustus_model.g23980.t1
Valid prediction for GlimmerHMM_glimmerT_35957-T1
Valid prediction for GlimmerHMM_glimmerT_35964-T1
Valid prediction for pasa_asmbl_15124.p1
Valid prediction for snap_scaffold_15-snap.884-T1
Valid prediction for snap_scaffold_15-snap.876-T1
Valid prediction for GlimmerHMM_glimmerT_35973-T1
Couldn't classify 19417, 19650
Sorry, prediction pasa_asmbl_15117.p1 fails validation.
(TGT)	 CC	19417-19650	GT	AGG
(ATG)	 AG	20289-20447	GC	AGG
add_exon() Sorry, pasa_asmbl_15117.p1 20289-20447-initial-1 is invalid.
-recovered pasa_asmbl_15117.p1, initial, 20289, 20447
-recovered pasa_asmbl_15117.p1, terminal, 20289, 20447
-recovered pasa_asmbl_15117.p1, internal, 20289, 20447
Valid prediction for snap_scaffold_15-snap.871-T1
Valid prediction for snap_scaffold_15-snap.849-T1
Valid prediction for HiQ_model.g23982.t1
Valid prediction for snap_scaffold_15-snap.859-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_15-snap.862-T1
Valid prediction for GlimmerHMM_glimmerT_35950-T1
Valid prediction for HiQ_model.g23987.t1
Valid prediction for snap_scaffold_15-snap.882-T1
Valid prediction for GlimmerHMM_glimmerT_35952-T1
Valid prediction for GlimmerHMM_glimmerT_35972-T1
Valid prediction for pasa_asmbl_14134.p1
Valid prediction for snap_scaffold_15-snap.855-T1
Valid prediction for snap_scaffold_15-snap.868-T1
Valid prediction for snap_scaffold_15-snap.881-T1
Valid prediction for CodingQuarry_transcript_17969-T1
Valid prediction for snap_scaffold_15-snap.857-T1
Couldn't classify 26273, 26291
Sorry, prediction pasa_asmbl_14128.p1 fails validation.
(CAC)	 AA	26273-26291	GT	AGG
(GGG)	 AG	26627-26746	GT	AGG
(GAG)	 AG	27055-27174	GT	AGG
(GCT)	 AG	27354-27454	AC	AGA
-recovered pasa_asmbl_14128.p1, terminal, 27354, 27454
-recovered pasa_asmbl_14128.p1, internal, 26627, 26746
-recovered pasa_asmbl_14128.p1, internal, 27055, 27174
Valid prediction for GlimmerHMM_glimmerT_35966-T1
Valid prediction for GlimmerHMM_glimmerT_35960-T1
Valid prediction for GlimmerHMM_glimmerT_35954-T1
Valid prediction for GlimmerHMM_glimmerT_35953-T1
Valid prediction for Augustus_model.g23976.t1
Valid prediction for GlimmerHMM_glimmerT_35975-T1
Valid prediction for snap_scaffold_15-snap.858-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_17968-T1
Valid prediction for GlimmerHMM_glimmerT_35959-T1
Valid prediction for snap_scaffold_15-snap.880-T1
Valid prediction for HiQ_model.g23990.t1
Valid prediction for CodingQuarry_transcript_17965-T1
Valid prediction for GlimmerHMM_glimmerT_35965-T1
Valid prediction for snap_scaffold_15-snap.864-T1
Valid prediction for GlimmerHMM_glimmerT_35970-T1
Valid prediction for HiQ_model.g23986.t1
Valid prediction for GlimmerHMM_glimmerT_35962-T1
Valid prediction for Augustus_model.g23989.t1
Valid prediction for snap_scaffold_15-snap.847-T1
Valid prediction for snap_scaffold_15-snap.848-T1
Valid prediction for Augustus_model.g23973.t1
Valid prediction for snap_scaffold_15-snap.875-T1
Valid prediction for Augustus_model.g23975.t1
Valid prediction for pasa_asmbl_14132.p1
Valid prediction for CodingQuarry_transcript_17971-T1
Valid prediction for snap_scaffold_15-snap.865-T1
Valid prediction for snap_scaffold_15-snap.867-T1
Valid prediction for Augustus_model.g23981.t1
Valid prediction for Augustus_model.g23988.t1
Valid prediction for snap_scaffold_15-snap.877-T1
Valid prediction for pasa_asmbl_14124.p1
Valid prediction for GlimmerHMM_glimmerT_35949-T1
Valid prediction for GlimmerHMM_glimmerT_35967-T1
Valid prediction for CodingQuarry_transcript_17970-T1
Valid prediction for GlimmerHMM_glimmerT_35956-T1
Valid prediction for Augustus_model.g23983.t1
Valid prediction for snap_scaffold_15-snap.886-T1
Valid prediction for snap_scaffold_15-snap.851-T1
Valid prediction for snap_scaffold_15-snap.856-T1
Valid prediction for snap_scaffold_15-snap.874-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17248, rend_intergenic: 13519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36227, rend_intergenic: 23245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69863, rend_intergenic: 63672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82532, rend_intergenic: 76456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93476, rend_intergenic: 85913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101325, rend_intergenic: 94463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117739, rend_intergenic: 105154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181463, rend_intergenic: 178616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186221
-exon list size: 420


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.0    
4.3    
4.5    
4.7    
5.0    
5.2    
5.5    
5.7    
5.9    
6.2    
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6.9    
7.1    
7.3    
7.6    
7.8    
8.1    
8.3    
8.5    
8.8    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.4    
10.7    
10.9    
11.1    
11.4    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.0    
13.3    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.4    
16.6    
16.8    
17.1    
17.3    
17.5    
17.8    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.3    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.7    
51.9    
52.1    
52.4    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.9    
57.1    
57.3    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
64.9    
65.2    
65.4    
65.6    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.7    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 17248, rend_intergenic: 13519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36227, rend_intergenic: 23245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69863, rend_intergenic: 63672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82532, rend_intergenic: 76456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93476, rend_intergenic: 85913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101325, rend_intergenic: 94463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117739, rend_intergenic: 105154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181463, rend_intergenic: 178616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support