-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_3332257-3437344

-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 GeneMark_model.104514_t
Valid prediction for HiQ_model.g39902.t1
Valid prediction for GeneMark_model.104510_t
Valid prediction for Augustus_model.g39905.t1
Couldn't classify 87752, 87860
Couldn't classify 88764, 88824
Sorry, prediction pasa_asmbl_38179.p1 fails validation.
(CCT)	 GG	87752-87860	GT	CAG
(AGT)	 AG	88101-88233	GT	CGG
(GAC)	 AG	88764-88824	AG	ACA
-recovered pasa_asmbl_38179.p1, internal, 88101, 88233
Valid prediction for GlimmerHMM_glimmerT_59949-T1
Valid prediction for GlimmerHMM_glimmerT_59948-T1
Valid prediction for GeneMark_model.104521_t
Valid prediction for GeneMark_model.104515_t
Valid prediction for Augustus_model.g39897.t1
Valid prediction for GlimmerHMM_glimmerT_59944-T1
Valid prediction for HiQ_model.g39907.t1
Valid prediction for pasa_asmbl_38177.p1
Valid prediction for GlimmerHMM_glimmerT_59953-T1
Valid prediction for snap_scaffold_28-snap.844-T1
Valid prediction for GeneMark_model.104499_t
Valid prediction for GlimmerHMM_glimmerT_59934-T1
Valid prediction for GlimmerHMM_glimmerT_59940-T1
Valid prediction for GeneMark_model.104496_t
Valid prediction for snap_scaffold_28-snap.852-T1
Valid prediction for GeneMark_model.104506_t
Valid prediction for Augustus_model.g39898.t1
Valid prediction for GlimmerHMM_glimmerT_59945-T1
Valid prediction for snap_scaffold_28-snap.837-T1
Valid prediction for Augustus_model.g39899.t1
Valid prediction for GlimmerHMM_glimmerT_59938-T1
Valid prediction for GlimmerHMM_glimmerT_59937-T1
Valid prediction for GlimmerHMM_glimmerT_59929-T1
Valid prediction for snap_scaffold_28-snap.851-T1
Valid prediction for GeneMark_model.104497_t
Valid prediction for GlimmerHMM_glimmerT_59952-T1
Valid prediction for snap_scaffold_28-snap.840-T1
Valid prediction for GlimmerHMM_glimmerT_59947-T1
Valid prediction for GlimmerHMM_glimmerT_59946-T1
Valid prediction for GeneMark_model.104513_t
Couldn't classify 54166, 54204
Sorry, prediction pasa_asmbl_38175.p1 fails validation.
(CTT)	 TC	54166-54204	GT	AGG
(GTC)	 AG	54911-54955	GT	AGG
(ACG)	 AG	55198-55419	GC	AGG
(GCT)	 AG	55444-55749	GT	AGG
(GTC)	 AG	56357-56398	GT	TGG
(GTG)	 AG	56769-56840	GT	AGG
(GTC)	 AG	56979-57092	GT	AGG
(GTG)	 AG	57304-57408	GT	AGG
(GCT)	 AG	58199-58237	GT	AGG
(GAC)	 AG	58377-58505	GT	TGG
(GAA)	 AG	58891-58950	GT	AGG
-recovered pasa_asmbl_38175.p1, terminal, 58891, 58950
-recovered pasa_asmbl_38175.p1, internal, 54911, 54955
-recovered pasa_asmbl_38175.p1, internal, 55198, 55419
-recovered pasa_asmbl_38175.p1, internal, 55444, 55749
-recovered pasa_asmbl_38175.p1, internal, 56357, 56398
-recovered pasa_asmbl_38175.p1, internal, 56769, 56840
-recovered pasa_asmbl_38175.p1, internal, 56979, 57092
-recovered pasa_asmbl_38175.p1, internal, 57304, 57408
-recovered pasa_asmbl_38175.p1, internal, 58199, 58237
-recovered pasa_asmbl_38175.p1, internal, 58377, 58505
-recovered pasa_asmbl_38175.p1, internal, 58891, 58950
Valid prediction for CodingQuarry_transcript_43512-T1
Valid prediction for GlimmerHMM_glimmerT_59943-T1
Valid prediction for GlimmerHMM_glimmerT_59954-T1
Valid prediction for snap_scaffold_28-snap.835-T1
Valid prediction for GeneMark_model.104508_t
Valid prediction for GlimmerHMM_glimmerT_59950-T1
Valid prediction for GeneMark_model.104501_t
Valid prediction for GeneMark_model.104518_t
Valid prediction for snap_scaffold_28-snap.838-T1
Valid prediction for snap_scaffold_28-snap.842-T1
Valid prediction for GlimmerHMM_glimmerT_59933-T1
Valid prediction for GlimmerHMM_glimmerT_59932-T1
Valid prediction for snap_scaffold_28-snap.850-T1
Valid prediction for GlimmerHMM_glimmerT_59951-T1
Valid prediction for snap_scaffold_28-snap.856-T1
Valid prediction for GeneMark_model.104511_t
Valid prediction for Augustus_model.g39903.t1
Valid prediction for GeneMark_model.104504_t
Valid prediction for GlimmerHMM_glimmerT_59930-T1
Valid prediction for Augustus_model.g39908.t1
Valid prediction for snap_scaffold_28-snap.849-T1
Couldn't classify 71868, 72004
Sorry, prediction pasa_asmbl_38178.p1 fails validation.
(ACA)	 AA	71868-72004	GT	AGG
(AAT)	 AG	72335-72530	GT	AGG
(GAC)	 AG	72699-72865	GT	TAG
(TGA)	 AG	72971-73111	GT	AGG
(ATG)	 AG	73369-73547	GT	AAG
(ACT)	 AG	73652-73765	GT	GGG
(GGC)	 AG	74088-74191	GT	AGG
(GTG)	 AG	74544-74735	CG	GAC
add_exon() Sorry, pasa_asmbl_38178.p1 73369-73547-initial-1 is invalid.
-recovered pasa_asmbl_38178.p1, initial, 73369, 73547
-recovered pasa_asmbl_38178.p1, terminal, 74544, 74735
-recovered pasa_asmbl_38178.p1, internal, 72335, 72530
-recovered pasa_asmbl_38178.p1, internal, 72699, 72865
-recovered pasa_asmbl_38178.p1, internal, 72971, 73111
-recovered pasa_asmbl_38178.p1, internal, 73369, 73547
-recovered pasa_asmbl_38178.p1, internal, 73652, 73765
-recovered pasa_asmbl_38178.p1, internal, 74088, 74191
Couldn't classify 48449, 48976
Sorry, prediction pasa_asmbl_38172.p2 fails validation.
(ATG)	 AA	46084-46128	GT	TGG
(CAG)	 AG	48449-48976	GT	AGG
-recovered pasa_asmbl_38172.p2, initial, 46084, 46128
-recovered pasa_asmbl_38172.p2, internal, 48449, 48976
Valid prediction for HiQ_model.g39906.t1
Valid prediction for GeneMark_model.104516_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 GlimmerHMM_glimmerT_59935-T1
Valid prediction for pasa_asmbl_37475.p1
Valid prediction for GeneMark_model.104520_t
Valid prediction for snap_scaffold_28-snap.855-T1
Valid prediction for GeneMark_model.104500_t
Valid prediction for snap_scaffold_28-snap.848-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.104512_t
Valid prediction for HiQ_model.g39904.t1
Valid prediction for GeneMark_model.104519_t
Valid prediction for snap_scaffold_28-snap.841-T1
Valid prediction for GeneMark_model.104495_t
Valid prediction for GeneMark_model.104517_t
Valid prediction for GeneMark_model.104505_t
Valid prediction for snap_scaffold_28-snap.846-T1
Valid prediction for GeneMark_model.104507_t
Valid prediction for snap_scaffold_28-snap.836-T1
Valid prediction for GeneMark_model.104498_t
Valid prediction for snap_scaffold_28-snap.843-T1
Valid prediction for snap_scaffold_28-snap.845-T1
Valid prediction for GlimmerHMM_glimmerT_59942-T1
Valid prediction for snap_scaffold_28-snap.854-T1
Valid prediction for GlimmerHMM_glimmerT_59939-T1
Valid prediction for GlimmerHMM_glimmerT_59936-T1
Valid prediction for CodingQuarry_transcript_43511-T1
Valid prediction for GlimmerHMM_glimmerT_59941-T1
Valid prediction for snap_scaffold_28-snap.847-T1
Couldn't classify 72454, 72489
Sorry, prediction pasa_asmbl_37474.p1 fails validation.
(GAG)	 CG	72454-72489	GT	AGG
(TGG)	 AG	73923-73989	GT	CAG
(GTC)	 AG	74928-75076	GT	AGG
(GTG)	 AG	75198-75343	GT	AGG
(GAT)	 AG	75689-75763	GT	AGG
(ACT)	 AG	75873-75962	GT	AAG
(AGA)	 AG	76108-76201	GT	TGG
(GTG)	 AG	76330-76445	GT	AGG
(GCT)	 AG	76988-77043	GT	GGG
(GAA)	 AG	77176-77261	GT	AGG
(TAC)	 AG	77523-77651	GT	AGG
(GAG)	 AG	77754-77833	GT	TGG
(GGA)	 AG	78201-78306	CA	GAC
-recovered pasa_asmbl_37474.p1, terminal, 78201, 78306
-recovered pasa_asmbl_37474.p1, internal, 73923, 73989
-recovered pasa_asmbl_37474.p1, internal, 74928, 75076
-recovered pasa_asmbl_37474.p1, internal, 75198, 75343
-recovered pasa_asmbl_37474.p1, internal, 75689, 75763
-recovered pasa_asmbl_37474.p1, internal, 75873, 75962
-recovered pasa_asmbl_37474.p1, internal, 76108, 76201
-recovered pasa_asmbl_37474.p1, internal, 76330, 76445
-recovered pasa_asmbl_37474.p1, internal, 76988, 77043
-recovered pasa_asmbl_37474.p1, internal, 77176, 77261
-recovered pasa_asmbl_37474.p1, internal, 77523, 77651
-recovered pasa_asmbl_37474.p1, internal, 77754, 77833
Valid prediction for GlimmerHMM_glimmerT_59931-T1
Valid prediction for pasa_asmbl_37477.p1
Valid prediction for GeneMark_model.104509_t
Valid prediction for Augustus_model.g39896.t1
Valid prediction for GeneMark_model.104503_t
Valid prediction for GeneMark_model.104502_t
Valid prediction for snap_scaffold_28-snap.839-T1
Valid prediction for HiQ_model.g39901.t1
Valid prediction for HiQ_model.g39900.t1
Valid prediction for snap_scaffold_28-snap.853-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26138, rend_intergenic: 26022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32728, rend_intergenic: 26414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38684, rend_intergenic: 35413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55881, rend_intergenic: 48401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95662, rend_intergenic: 78708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97080, rend_intergenic: 95665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 105088
-exon list size: 452


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.5    
1.8    
2.0    
2.2    
2.4    
2.6    
2.9    
3.1    
3.3    
3.5    
3.7    
4.0    
4.2    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.8    
7.0    
7.3    
7.5    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.3    
9.5    
9.7    
9.9    
10.1    
10.4    
10.6    
10.8    
11.0    
11.2    
11.5    
11.7    
11.9    
12.1    
12.3    
12.6    
12.8    
13.0    
13.2    
13.4    
13.7    
13.9    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.4    
15.6    
15.9    
16.1    
16.3    
16.5    
16.7    
17.0    
17.2    
17.4    
17.6    
17.8    
18.1    
18.3    
18.5    
18.7    
18.9    
19.2    
19.4    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.5    
53.7    
54.0    
54.2    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.0    
59.3    
59.5    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.4    
65.6    
65.9    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.3    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 26138, rend_intergenic: 26022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32728, rend_intergenic: 26414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38684, rend_intergenic: 35413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55881, rend_intergenic: 48401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95662, rend_intergenic: 78708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97080, rend_intergenic: 95665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support