-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_2868123-3065194

-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_5-snap.575-T1
Valid prediction for GeneMark_model.20004_t
Valid prediction for snap_scaffold_5-snap.583-T1
Valid prediction for Augustus_model.g7817.t1
Valid prediction for GeneMark_model.19996_t
Valid prediction for GlimmerHMM_glimmerT_11886-T1
Valid prediction for snap_scaffold_5-snap.572-T1
Valid prediction for GeneMark_model.19994_t
Valid prediction for GeneMark_model.20018_t
Valid prediction for GlimmerHMM_glimmerT_11891-T1
Valid prediction for GlimmerHMM_glimmerT_11883-T1
Valid prediction for GeneMark_model.20019_t
Couldn't classify 118077, 118125
Couldn't classify 119593, 119627
Sorry, prediction pasa_asmbl_45012.p1 fails validation.
(AAG)	 CA	118077-118125	GT	AAG
(TTG)	 AG	118394-118551	GT	AGG
(TCT)	 AG	118908-119103	GT	AGG
(GGG)	 AG	119593-119627	GT	AGG
-recovered pasa_asmbl_45012.p1, internal, 118394, 118551
-recovered pasa_asmbl_45012.p1, internal, 118908, 119103
-recovered pasa_asmbl_45012.p1, internal, 119593, 119627
Valid prediction for GeneMark_model.19986_t
Valid prediction for snap_scaffold_5-snap.590-T1
Valid prediction for snap_scaffold_5-snap.589-T1
Valid prediction for GlimmerHMM_glimmerT_11884-T1
Valid prediction for Augustus_model.g7808.t1
Valid prediction for snap_scaffold_5-snap.571-T1
Valid prediction for GeneMark_model.20028_t
Valid prediction for Augustus_model.g7811.t1
Valid prediction for GeneMark_model.19991_t
Valid prediction for GlimmerHMM_glimmerT_11889-T1
Valid prediction for Augustus_model.g7810.t1
Valid prediction for GeneMark_model.20022_t
Valid prediction for GlimmerHMM_glimmerT_11893-T1
Valid prediction for GeneMark_model.19990_t
Valid prediction for GeneMark_model.20024_t
Valid prediction for GeneMark_model.20012_t
Valid prediction for GeneMark_model.19992_t
Valid prediction for Augustus_model.g7812.t1
Valid prediction for GeneMark_model.20011_t
Valid prediction for GlimmerHMM_glimmerT_11894-T1
Couldn't classify 47943, 48479
Sorry, prediction pasa_asmbl_45034.p1 fails validation.
(ATC)	 GC	47943-48479	CA	CCC
Valid prediction for GeneMark_model.20020_t
Valid prediction for GeneMark_model.19988_t
Valid prediction for GeneMark_model.20016_t
Valid prediction for GlimmerHMM_glimmerT_11899-T1
Valid prediction for snap_scaffold_5-snap.573-T1
Valid prediction for snap_scaffold_5-snap.587-T1
Valid prediction for Augustus_model.g7809.t1
Valid prediction for GeneMark_model.19998_t
Valid prediction for snap_scaffold_5-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_11895-T1
Valid prediction for Augustus_model.g7815.t1
Valid prediction for GeneMark_model.20030_t
Valid prediction for snap_scaffold_5-snap.595-T1
Couldn't classify 26884, 27032
Couldn't classify 28599, 29124
Sorry, prediction pasa_asmbl_43866.p1 fails validation.
(AGC)	 CC	26884-27032	GT	AGG
(GCG)	 AG	28599-29124	GG	CCG
Couldn't classify 46393, 46710
Sorry, prediction pasa_asmbl_43868.p2 fails validation.
(TTC)	 CA	46393-46710	TC	CCT
Valid prediction for GeneMark_model.20008_t
Valid prediction for GeneMark_model.20006_t
Valid prediction for GeneMark_model.20010_t
Valid prediction for GeneMark_model.20013_t
Valid prediction for GeneMark_model.20015_t
Valid prediction for GeneMark_model.20002_t
Valid prediction for snap_scaffold_5-snap.577-T1
Valid prediction for GlimmerHMM_glimmerT_11882-T1
Valid prediction for GeneMark_model.19985_t

-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_5-snap.591-T1
Valid prediction for Augustus_model.g7814.t1
Valid prediction for snap_scaffold_5-snap.608-T1
Valid prediction for GeneMark_model.20027_t
Valid prediction for snap_scaffold_5-snap.607-T1
Valid prediction for Augustus_model.g7816.t1
Valid prediction for snap_scaffold_5-snap.604-T1
Valid prediction for GlimmerHMM_glimmerT_11898-T1
Valid prediction for GeneMark_model.20021_t
Valid prediction for GlimmerHMM_glimmerT_11887-T1
Valid prediction for snap_scaffold_5-snap.582-T1
Valid prediction for snap_scaffold_5-snap.579-T1
Valid prediction for GeneMark_model.20009_t
Valid prediction for Augustus_model.g7822.t1
Valid prediction for Augustus_model.g7813.t1
Valid prediction for CodingQuarry_transcript_51877-T1
Valid prediction for snap_scaffold_5-snap.594-T1
Valid prediction for Augustus_model.g7818.t1
Valid prediction for GeneMark_model.20005_t
Valid prediction for snap_scaffold_5-snap.585-T1
Valid prediction for CodingQuarry_transcript_51878-T1
Valid prediction for GeneMark_model.19999_t
Valid prediction for snap_scaffold_5-snap.606-T1
Valid prediction for GeneMark_model.20014_t
Valid prediction for GlimmerHMM_glimmerT_11885-T1
Valid prediction for snap_scaffold_5-snap.576-T1
Valid prediction for GeneMark_model.20025_t
Valid prediction for snap_scaffold_5-snap.581-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for HiQ_model.g7821.t1
Valid prediction for GlimmerHMM_glimmerT_11897-T1
Valid prediction for snap_scaffold_5-snap.600-T1
Valid prediction for snap_scaffold_5-snap.603-T1
Valid prediction for snap_scaffold_5-snap.593-T1
Valid prediction for snap_scaffold_5-snap.598-T1
Couldn't classify 45218, 45227
Sorry, prediction CodingQuarry_transcript_51879-T1 fails validation.
(ATG)	 AG	43313-43369	GT	AGG
(GAT)	 AG	43530-43622	GT	TGG
(TAC)	 AG	43722-43790	GT	AGG
(ATC)	 AG	43985-44078	GT	AGG
(AGG)	 AG	44186-44259	GT	CAG
(GAA)	 AG	44453-44633	GT	TGG
(GAG)	 AG	44725-44789	GT	AGG
(AAC)	 AG	44891-44967	GT	AGG
(TTC)	 AT	45218-45227	CT	AAC
-recovered CodingQuarry_transcript_51879-T1, initial, 43313, 43369
-recovered CodingQuarry_transcript_51879-T1, internal, 43313, 43369
-recovered CodingQuarry_transcript_51879-T1, internal, 43530, 43622
-recovered CodingQuarry_transcript_51879-T1, internal, 43722, 43790
-recovered CodingQuarry_transcript_51879-T1, internal, 43985, 44078
-recovered CodingQuarry_transcript_51879-T1, internal, 44186, 44259
-recovered CodingQuarry_transcript_51879-T1, internal, 44453, 44633
-recovered CodingQuarry_transcript_51879-T1, internal, 44725, 44789
-recovered CodingQuarry_transcript_51879-T1, internal, 44891, 44967
Valid prediction for snap_scaffold_5-snap.574-T1
Valid prediction for snap_scaffold_5-snap.602-T1
Valid prediction for GlimmerHMM_glimmerT_11900-T1
Valid prediction for GlimmerHMM_glimmerT_11892-T1
Valid prediction for Augustus_model.g7819.t1
Valid prediction for GeneMark_model.20003_t
Valid prediction for snap_scaffold_5-snap.592-T1
Valid prediction for snap_scaffold_5-snap.588-T1
Valid prediction for pasa_asmbl_45294.p1
Valid prediction for GeneMark_model.20031_t
Valid prediction for GlimmerHMM_glimmerT_11890-T1
Valid prediction for GeneMark_model.20029_t
Valid prediction for pasa_asmbl_45293.p1
Valid prediction for GeneMark_model.19995_t
Valid prediction for GeneMark_model.20026_t
Valid prediction for GeneMark_model.19993_t
Valid prediction for snap_scaffold_5-snap.601-T1
Valid prediction for GeneMark_model.19997_t
Valid prediction for GlimmerHMM_glimmerT_11896-T1
Valid prediction for snap_scaffold_5-snap.570-T1
Valid prediction for GeneMark_model.19989_t
Valid prediction for snap_scaffold_5-snap.597-T1
Valid prediction for snap_scaffold_5-snap.584-T1
Valid prediction for snap_scaffold_5-snap.578-T1
Valid prediction for HiQ_model.g7820.t1
Valid prediction for snap_scaffold_5-snap.586-T1
Valid prediction for GeneMark_model.20001_t
Valid prediction for GeneMark_model.19987_t
Couldn't classify 127443, 127516
Couldn't classify 128561, 129059
Sorry, prediction pasa_asmbl_45290.p1 fails validation.
(CGC)	 AC	127443-127516	GT	AGG
(GAG)	 AG	128561-129059	GA	TGG
Valid prediction for GeneMark_model.20017_t
Valid prediction for snap_scaffold_5-snap.580-T1
Valid prediction for snap_scaffold_5-snap.605-T1
Valid prediction for snap_scaffold_5-snap.599-T1
Valid prediction for GeneMark_model.20032_t
Valid prediction for GeneMark_model.20023_t
Valid prediction for GlimmerHMM_glimmerT_11888-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6895, rend_intergenic: 2840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20662, rend_intergenic: 13210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31909, rend_intergenic: 29346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32399, rend_intergenic: 31925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48999, rend_intergenic: 33400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68574, rend_intergenic: 68008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80582, rend_intergenic: 77620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80956, rend_intergenic: 80707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83887, rend_intergenic: 81147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103319, rend_intergenic: 96908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113509, rend_intergenic: 110931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197072
-exon list size: 579


building trellis

0.2    
0.3    
0.5    
0.7    
0.9    
1.0    
1.2    
1.4    
1.5    
1.7    
1.9    
2.1    
2.2    
2.4    
2.6    
2.8    
2.9    
3.1    
3.3    
3.4    
3.6    
3.8    
4.0    
4.1    
4.3    
4.5    
4.6    
4.8    
5.0    
5.2    
5.3    
5.5    
5.7    
5.9    
6.0    
6.2    
6.4    
6.5    
6.7    
6.9    
7.1    
7.2    
7.4    
7.6    
7.7    
7.9    
8.1    
8.3    
8.4    
8.6    
8.8    
9.0    
9.1    
9.3    
9.5    
9.6    
9.8    
10.0    
10.2    
10.3    
10.5    
10.7    
10.8    
11.0    
11.2    
11.4    
11.5    
11.7    
11.9    
12.0    
12.2    
12.4    
12.6    
12.7    
12.9    
13.1    
13.3    
13.4    
13.6    
13.8    
13.9    
14.1    
14.3    
14.5    
14.6    
14.8    
15.0    
15.1    
15.3    
15.5    
15.7    
15.8    
16.0    
16.2    
16.4    
16.5    
16.7    
16.9    
17.0    
17.2    
17.4    
17.6    
17.7    
17.9    
18.1    
18.2    
18.4    
18.6    
18.8    
18.9    
19.1    
19.3    
19.4    
19.6    
19.8    
20.0    
20.1    
20.3    
20.5    
20.7    
20.8    
21.0    
21.2    
21.3    
21.5    
21.7    
21.9    
22.0    
22.2    
22.4    
22.5    
22.7    
22.9    
23.1    
23.2    
23.4    
23.6    
23.8    
23.9    
24.1    
24.3    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.6    
25.8    
26.0    
26.2    
26.3    
26.5    
26.7    
26.9    
27.0    
27.2    
27.4    
27.5    
27.7    
27.9    
28.1    
28.2    
28.4    
28.6    
28.7    
28.9    
29.1    
29.3    
29.4    
29.6    
29.8    
29.9    
30.1    
30.3    
30.5    
30.6    
30.8    
31.0    
31.2    
31.3    
31.5    
31.7    
31.8    
32.0    
32.2    
32.4    
32.5    
32.7    
32.9    
33.0    
33.2    
33.4    
33.6    
33.7    
33.9    
34.1    
34.3    
34.4    
34.6    
34.8    
34.9    
35.1    
35.3    
35.5    
35.6    
35.8    
36.0    
36.1    
36.3    
36.5    
36.7    
36.8    
37.0    
37.2    
37.3    
37.5    
37.7    
37.9    
38.0    
38.2    
38.4    
38.6    
38.7    
38.9    
39.1    
39.2    
39.4    
39.6    
39.8    
39.9    
40.1    
40.3    
40.4    
40.6    
40.8    
41.0    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.3    
42.5    
42.7    
42.9    
43.0    
43.2    
43.4    
43.5    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.8    
44.9    
45.1    
45.3    
45.4    
45.6    
45.8    
46.0    
46.1    
46.3    
46.5    
46.6    
46.8    
47.0    
47.2    
47.3    
47.5    
47.7    
47.8    
48.0    
48.2    
48.4    
48.5    
48.7    
48.9    
49.1    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
50.9    
51.1    
51.3    
51.5    
51.6    
51.8    
52.0    
52.2    
52.3    
52.5    
52.7    
52.8    
53.0    
53.2    
53.4    
53.5    
53.7    
53.9    
54.0    
54.2    
54.4    
54.6    
54.7    
54.9    
55.1    
55.2    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.5    
56.6    
56.8    
57.0    
57.1    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
59.6    
59.7    
59.9    
60.1    
60.2    
60.4    
60.6    
60.8    
60.9    
61.1    
61.3    
61.4    
61.6    
61.8    
62.0    
62.1    
62.3    
62.5    
62.7    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.9    
64.0    
64.2    
64.4    
64.5    
64.7    
64.9    
65.1    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.6    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.4    
69.5    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.4    
71.6    
71.8    
71.9    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.8    
76.9    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 6895, rend_intergenic: 2840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20662, rend_intergenic: 13210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31909, rend_intergenic: 29346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32399, rend_intergenic: 31925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48999, rend_intergenic: 33400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68574, rend_intergenic: 68008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80582, rend_intergenic: 77620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80956, rend_intergenic: 80707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83887, rend_intergenic: 81147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103319, rend_intergenic: 96908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113509, rend_intergenic: 110931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support