-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_6028064-6190564

-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_28-snap.1360-T1
Valid prediction for GeneMark_model.105037_t
Valid prediction for GeneMark_model.105042_t
Valid prediction for GeneMark_model.105016_t
Valid prediction for Augustus_model.g40188.t1
Valid prediction for GeneMark_model.105044_t
Valid prediction for GlimmerHMM_glimmerT_60339-T1
Valid prediction for GeneMark_model.105012_t
Valid prediction for GlimmerHMM_glimmerT_60355-T1
Valid prediction for GlimmerHMM_glimmerT_60333-T1
Couldn't classify 36676, 36792
Sorry, prediction pasa_asmbl_38315.p1 fails validation.
(AGG)	 GC	36676-36792	GT	AGG
(GAG)	 AG	37023-37107	GT	AGG
(CTC)	 AG	38723-38794	GT	AGG
(ATG)	 AG	38904-39029	GT	AGG
(ATT)	 AG	39122-39239	GT	AGG
(CGA)	 AG	39614-39726	GT	AGG
(ACA)	 AG	40073-40232	GT	AGG
(GAA)	 AG	40330-40517	GT	AGG
(CCT)	 AG	40645-40858	GT	CAG
(ACT)	 AG	41163-41235	GC	AGG
(GTG)	 AG	41443-41640	GT	GGG
(GCA)	 AG	42153-42293	AG	GAA
-recovered pasa_asmbl_38315.p1, initial, 38904, 39029
-recovered pasa_asmbl_38315.p1, terminal, 42153, 42293
-recovered pasa_asmbl_38315.p1, internal, 37023, 37107
-recovered pasa_asmbl_38315.p1, internal, 38723, 38794
-recovered pasa_asmbl_38315.p1, internal, 38904, 39029
-recovered pasa_asmbl_38315.p1, internal, 39122, 39239
-recovered pasa_asmbl_38315.p1, internal, 39614, 39726
-recovered pasa_asmbl_38315.p1, internal, 40073, 40232
-recovered pasa_asmbl_38315.p1, internal, 40330, 40517
-recovered pasa_asmbl_38315.p1, internal, 40645, 40858
-recovered pasa_asmbl_38315.p1, internal, 41163, 41235
-recovered pasa_asmbl_38315.p1, internal, 41443, 41640
Valid prediction for GeneMark_model.105030_t
Valid prediction for GeneMark_model.105040_t
Valid prediction for GlimmerHMM_glimmerT_60340-T1
Valid prediction for snap_scaffold_28-snap.1373-T1
Valid prediction for Augustus_model.g40186.t1
Valid prediction for Augustus_model.g40191.t1
Valid prediction for snap_scaffold_28-snap.1369-T1
Valid prediction for GeneMark_model.105020_t
Valid prediction for GlimmerHMM_glimmerT_60353-T1
Valid prediction for GlimmerHMM_glimmerT_60348-T1
Valid prediction for GeneMark_model.105014_t
Valid prediction for Augustus_model.g40190.t1
Valid prediction for Augustus_model.g40181.t1
Valid prediction for Augustus_model.g40185.t1
Valid prediction for snap_scaffold_28-snap.1387-T1
Valid prediction for GlimmerHMM_glimmerT_60336-T1
Valid prediction for GeneMark_model.105033_t
Valid prediction for GeneMark_model.105035_t
Valid prediction for snap_scaffold_28-snap.1376-T1
Valid prediction for snap_scaffold_28-snap.1381-T1
Valid prediction for snap_scaffold_28-snap.1358-T1
Valid prediction for Augustus_model.g40193.t1
Valid prediction for Augustus_model.g40194.t1
Valid prediction for GlimmerHMM_glimmerT_60337-T1
Valid prediction for GlimmerHMM_glimmerT_60343-T1
Valid prediction for snap_scaffold_28-snap.1357-T1
Valid prediction for GeneMark_model.105047_t
Valid prediction for GeneMark_model.105022_t
Valid prediction for GlimmerHMM_glimmerT_60345-T1
Valid prediction for snap_scaffold_28-snap.1363-T1
Valid prediction for snap_scaffold_28-snap.1377-T1
Valid prediction for GeneMark_model.105031_t
Valid prediction for snap_scaffold_28-snap.1380-T1
Valid prediction for Augustus_model.g40182.t1
Valid prediction for CodingQuarry_transcript_43592-T1
Valid prediction for snap_scaffold_28-snap.1383-T1
Valid prediction for GeneMark_model.105007_t
Valid prediction for GeneMark_model.105008_t
Valid prediction for snap_scaffold_28-snap.1364-T1
Valid prediction for GeneMark_model.105038_t
Valid prediction for snap_scaffold_28-snap.1366-T1
Valid prediction for GeneMark_model.105025_t
Valid prediction for GlimmerHMM_glimmerT_60332-T1
Valid prediction for GeneMark_model.105046_t
Valid prediction for snap_scaffold_28-snap.1385-T1
Valid prediction for GeneMark_model.105034_t
Valid prediction for GlimmerHMM_glimmerT_60350-T1
Valid prediction for GlimmerHMM_glimmerT_60335-T1
Valid prediction for GeneMark_model.105018_t
Couldn't classify 36452, 36501
Sorry, prediction pasa_asmbl_38314.p1 fails validation.
(ATG)	 AC	28838-28966	GT	AGG
(GTC)	 AG	29208-29337	GT	GGG
(GGC)	 AG	29671-29796	GT	GGG
(CCA)	 AG	30109-30282	GT	AGG
(GGG)	 AG	32262-32399	GT	AGG
(AAG)	 AG	33938-34072	GT	AGG
(GTA)	 AG	35193-35312	GT	CGG
(GAG)	 AG	35622-35699	GT	AGG
(GCT)	 AG	36452-36501	CC	CCC
-recovered pasa_asmbl_38314.p1, initial, 28838, 28966
-recovered pasa_asmbl_38314.p1, internal, 29208, 29337
-recovered pasa_asmbl_38314.p1, internal, 29671, 29796
-recovered pasa_asmbl_38314.p1, internal, 30109, 30282
-recovered pasa_asmbl_38314.p1, internal, 32262, 32399
-recovered pasa_asmbl_38314.p1, internal, 33938, 34072
-recovered pasa_asmbl_38314.p1, internal, 35193, 35312
-recovered pasa_asmbl_38314.p1, internal, 35622, 35699
Valid prediction for GeneMark_model.105027_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 GeneMark_model.105041_t
Valid prediction for snap_scaffold_28-snap.1370-T1
Valid prediction for snap_scaffold_28-snap.1379-T1
Valid prediction for GlimmerHMM_glimmerT_60352-T1
Valid prediction for GeneMark_model.105019_t
Valid prediction for GeneMark_model.105029_t
Valid prediction for GlimmerHMM_glimmerT_60349-T1
Valid prediction for GeneMark_model.105043_t
Valid prediction for snap_scaffold_28-snap.1367-T1
Valid prediction for GeneMark_model.105026_t
Valid prediction for GlimmerHMM_glimmerT_60334-T1
Valid prediction for GeneMark_model.105017_t
Valid prediction for GeneMark_model.105021_t
Valid prediction for snap_scaffold_28-snap.1365-T1
Valid prediction for GeneMark_model.105024_t
Valid prediction for snap_scaffold_28-snap.1382-T1
Valid prediction for GeneMark_model.105045_t
Valid prediction for snap_scaffold_28-snap.1384-T1
Valid prediction for GeneMark_model.105032_t
Valid prediction for GeneMark_model.105023_t
Valid prediction for GlimmerHMM_glimmerT_60346-T1
Valid prediction for GlimmerHMM_glimmerT_60338-T1
Valid prediction for snap_scaffold_28-snap.1372-T1
Valid prediction for GeneMark_model.105015_t
Valid prediction for snap_scaffold_28-snap.1371-T1
Valid prediction for snap_scaffold_28-snap.1356-T1
Valid prediction for snap_scaffold_28-snap.1362-T1
Valid prediction for Augustus_model.g40192.t1
Valid prediction for snap_scaffold_28-snap.1386-T1
Valid prediction for Augustus_model.g40189.t1
Valid prediction for snap_scaffold_28-snap.1378-T1
Valid prediction for GlimmerHMM_glimmerT_60351-T1
Valid prediction for snap_scaffold_28-snap.1368-T1
Valid prediction for Augustus_model.g40187.t1
Valid prediction for GeneMark_model.105013_t
Valid prediction for snap_scaffold_28-snap.1375-T1
Valid prediction for snap_scaffold_28-snap.1388-T1
Valid prediction for GlimmerHMM_glimmerT_60341-T1
Valid prediction for GeneMark_model.105011_t
Valid prediction for snap_scaffold_28-snap.1374-T1
Valid prediction for GeneMark_model.105039_t
Valid prediction for GlimmerHMM_glimmerT_60342-T1
Valid prediction for snap_scaffold_28-snap.1359-T1
Valid prediction for GlimmerHMM_glimmerT_60347-T1
Valid prediction for Augustus_model.g40180.t1
Valid prediction for GeneMark_model.105036_t
Valid prediction for Augustus_model.g40183.t1
Valid prediction for Augustus_model.g40184.t1
Valid prediction for GeneMark_model.105009_t
Valid prediction for snap_scaffold_28-snap.1361-T1
Valid prediction for GlimmerHMM_glimmerT_60354-T1
Valid prediction for GlimmerHMM_glimmerT_60344-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 37768, rend_intergenic: 37765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 119908, rend_intergenic: 119905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28984, rend_intergenic: 28284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31170, rend_intergenic: 29054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43962, rend_intergenic: 37765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63451, rend_intergenic: 60273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67977, rend_intergenic: 65378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128797, rend_intergenic: 126363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144427, rend_intergenic: 142675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154326, rend_intergenic: 149813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154872, rend_intergenic: 154618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162501
-exon list size: 570


building trellis

0.2    
0.3    
0.5    
0.7    
0.9    
1.0    
1.2    
1.4    
1.6    
1.7    
1.9    
2.1    
2.3    
2.4    
2.6    
2.8    
3.0    
3.1    
3.3    
3.5    
3.7    
3.8    
4.0    
4.2    
4.4    
4.5    
4.7    
4.9    
5.1    
5.2    
5.4    
5.6    
5.8    
5.9    
6.1    
6.3    
6.5    
6.6    
6.8    
7.0    
7.2    
7.3    
7.5    
7.7    
7.9    
8.0    
8.2    
8.4    
8.6    
8.7    
8.9    
9.1    
9.3    
9.4    
9.6    
9.8    
10.0    
10.1    
10.3    
10.5    
10.7    
10.8    
11.0    
11.2    
11.4    
11.5    
11.7    
11.9    
12.1    
12.2    
12.4    
12.6    
12.8    
12.9    
13.1    
13.3    
13.5    
13.6    
13.8    
14.0    
14.2    
14.3    
14.5    
14.7    
14.9    
15.0    
15.2    
15.4    
15.6    
15.7    
15.9    
16.1    
16.3    
16.4    
16.6    
16.8    
17.0    
17.1    
17.3    
17.5    
17.7    
17.8    
18.0    
18.2    
18.4    
18.5    
18.7    
18.9    
19.1    
19.2    
19.4    
19.6    
19.8    
19.9    
20.1    
20.3    
20.5    
20.6    
20.8    
21.0    
21.2    
21.3    
21.5    
21.7    
21.9    
22.0    
22.2    
22.4    
22.6    
22.7    
22.9    
23.1    
23.3    
23.4    
23.6    
23.8    
24.0    
24.1    
24.3    
24.5    
24.7    
24.8    
25.0    
25.2    
25.3    
25.5    
25.7    
25.9    
26.0    
26.2    
26.4    
26.6    
26.7    
26.9    
27.1    
27.3    
27.4    
27.6    
27.8    
28.0    
28.1    
28.3    
28.5    
28.7    
28.8    
29.0    
29.2    
29.4    
29.5    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.8    
30.9    
31.1    
31.3    
31.5    
31.6    
31.8    
32.0    
32.2    
32.3    
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    
35.0    
35.1    
35.3    
35.5    
35.7    
35.8    
36.0    
36.2    
36.4    
36.5    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.5    
38.6    
38.8    
39.0    
39.2    
39.3    
39.5    
39.7    
39.9    
40.0    
40.2    
40.4    
40.6    
40.7    
40.9    
41.1    
41.3    
41.4    
41.6    
41.8    
42.0    
42.1    
42.3    
42.5    
42.7    
42.8    
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    
45.5    
45.6    
45.8    
46.0    
46.2    
46.3    
46.5    
46.7    
46.9    
47.0    
47.2    
47.4    
47.6    
47.7    
47.9    
48.1    
48.3    
48.4    
48.6    
48.8    
49.0    
49.1    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.6    
51.7    
51.9    
52.1    
52.3    
52.4    
52.6    
52.8    
53.0    
53.1    
53.3    
53.5    
53.7    
53.8    
54.0    
54.2    
54.4    
54.5    
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    
57.2    
57.3    
57.5    
57.7    
57.9    
58.0    
58.2    
58.4    
58.6    
58.7    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.8    
61.0    
61.2    
61.4    
61.5    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.6    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.9    
65.0    
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    
67.7    
67.8    
68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.2    
71.3    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.3    
77.4    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
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: GlimmerHMM lend_intergenic: 37768, rend_intergenic: 37765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 119908, rend_intergenic: 119905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28984, rend_intergenic: 28284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31170, rend_intergenic: 29054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43962, rend_intergenic: 37765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63451, rend_intergenic: 60273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67977, rend_intergenic: 65378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128797, rend_intergenic: 126363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144427, rend_intergenic: 142675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154326, rend_intergenic: 149813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154872, rend_intergenic: 154618  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