-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_7996151-8178572

-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.1584-T1
Valid prediction for GlimmerHMM_glimmerT_12518-T1
Valid prediction for snap_scaffold_5-snap.1576-T1
Valid prediction for GeneMark_model.21280_t
Valid prediction for GlimmerHMM_glimmerT_12512-T1
Valid prediction for CodingQuarry_transcript_52006-T1
Valid prediction for GeneMark_model.21287_t
Couldn't classify 96026, 96091
Couldn't classify 96827, 96889
Sorry, prediction pasa_asmbl_44189.p1 fails validation.
(GGG)	 CG	96026-96091	GT	AGG
(TGT)	 AG	96189-96355	GT	AGG
(GGT)	 AG	96552-96681	GT	TGG
(GTG)	 AG	96827-96889	AA	ACA
-recovered pasa_asmbl_44189.p1, internal, 96189, 96355
-recovered pasa_asmbl_44189.p1, internal, 96552, 96681
Valid prediction for GlimmerHMM_glimmerT_12511-T1
Valid prediction for pasa_asmbl_44185.p1
Valid prediction for GlimmerHMM_glimmerT_12521-T1
Valid prediction for snap_scaffold_5-snap.1579-T1
Valid prediction for snap_scaffold_5-snap.1577-T1
Valid prediction for GeneMark_model.21303_t
Valid prediction for Augustus_model.g8288.t1
Valid prediction for GlimmerHMM_glimmerT_12508-T1
Valid prediction for GeneMark_model.21283_t
Valid prediction for GeneMark_model.21286_t
Valid prediction for GeneMark_model.21292_t
Valid prediction for snap_scaffold_5-snap.1571-T1
Valid prediction for GlimmerHMM_glimmerT_12505-T1
Valid prediction for GeneMark_model.21290_t
Valid prediction for GlimmerHMM_glimmerT_12522-T1
Valid prediction for GlimmerHMM_glimmerT_12523-T1
Valid prediction for GeneMark_model.21278_t
Valid prediction for GlimmerHMM_glimmerT_12524-T1
Valid prediction for CodingQuarry_transcript_52005-T1
Valid prediction for GlimmerHMM_glimmerT_12529-T1
Valid prediction for pasa_asmbl_44191.p1
Valid prediction for Augustus_model.g8291.t1
Valid prediction for snap_scaffold_5-snap.1587-T1
Valid prediction for GeneMark_model.21281_t
Valid prediction for GeneMark_model.21299_t
Valid prediction for Augustus_model.g8289.t1
Valid prediction for GeneMark_model.21298_t
Valid prediction for GeneMark_model.21295_t
Valid prediction for snap_scaffold_5-snap.1575-T1
Valid prediction for GeneMark_model.21293_t
Valid prediction for GlimmerHMM_glimmerT_12530-T1
Valid prediction for snap_scaffold_5-snap.1566-T1
Valid prediction for GlimmerHMM_glimmerT_12515-T1
Valid prediction for GlimmerHMM_glimmerT_12509-T1
Valid prediction for GlimmerHMM_glimmerT_12517-T1
Valid prediction for CodingQuarry_transcript_52009-T1
Valid prediction for GeneMark_model.21308_t
Valid prediction for GeneMark_model.21297_t
Valid prediction for snap_scaffold_5-snap.1586-T1
Valid prediction for GlimmerHMM_glimmerT_12525-T1
Valid prediction for pasa_asmbl_44188.p1
Valid prediction for CodingQuarry_transcript_52011-T1
Valid prediction for snap_scaffold_5-snap.1583-T1
Valid prediction for CodingQuarry_transcript_52007-T1
Valid prediction for GlimmerHMM_glimmerT_12531-T1
Valid prediction for snap_scaffold_5-snap.1574-T1
Valid prediction for HiQ_model.g8295.t1
Valid prediction for GlimmerHMM_glimmerT_12519-T1
Couldn't classify 141884, 142077
Sorry, prediction pasa_asmbl_44198.p1 fails validation.
(GGG)	 CT	141884-142077	GT	AGG
(GAC)	 AG	142209-142371	GT	AAG
(ACA)	 AG	144277-144401	GT	AGG
(CCC)	 AG	144666-144774	GT	CGG
(GAG)	 AG	144954-145061	GT	AGG
(GTG)	 AG	145540-145693	GT	AGG
(GTG)	 AG	145792-145859	GT	AGG
(GAG)	 AG	146002-146123	GT	AGG
(GAT)	 AG	146433-146664	GT	ACG
(GAG)	 AG	147614-147716	GT	TGG
(AGG)	 AG	147807-148027	GT	AGG
(GTG)	 AG	148160-148315	GT	TGG
(ATC)	 AG	148421-148617	GT	CAG
(GGA)	 AG	149087-149221	GT	AGG
(GAA)	 AG	149442-149511	AT	AGA
-recovered pasa_asmbl_44198.p1, terminal, 149442, 149511
-recovered pasa_asmbl_44198.p1, internal, 142209, 142371
-recovered pasa_asmbl_44198.p1, internal, 144277, 144401
-recovered pasa_asmbl_44198.p1, internal, 144666, 144774
-recovered pasa_asmbl_44198.p1, internal, 144954, 145061
-recovered pasa_asmbl_44198.p1, internal, 145540, 145693
-recovered pasa_asmbl_44198.p1, internal, 145792, 145859
-recovered pasa_asmbl_44198.p1, internal, 146002, 146123
-recovered pasa_asmbl_44198.p1, internal, 146433, 146664
-recovered pasa_asmbl_44198.p1, internal, 147614, 147716
-recovered pasa_asmbl_44198.p1, internal, 147807, 148027
-recovered pasa_asmbl_44198.p1, internal, 148160, 148315
-recovered pasa_asmbl_44198.p1, internal, 148421, 148617
-recovered pasa_asmbl_44198.p1, internal, 149087, 149221
Valid prediction for HiQ_model.g8296.t1
Valid prediction for GeneMark_model.21289_t
Valid prediction for GlimmerHMM_glimmerT_12513-T1
Valid prediction for CodingQuarry_transcript_52010-T1
Valid prediction for GeneMark_model.21304_t
Valid prediction for GlimmerHMM_glimmerT_12507-T1
Valid prediction for GeneMark_model.21302_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.1569-T1
Valid prediction for GeneMark_model.21306_t
Valid prediction for GeneMark_model.21294_t
Valid prediction for GlimmerHMM_glimmerT_12516-T1
Valid prediction for GeneMark_model.21300_t
Valid prediction for GlimmerHMM_glimmerT_12535-T1
Valid prediction for GlimmerHMM_glimmerT_12526-T1
Valid prediction for GeneMark_model.21279_t
Valid prediction for GeneMark_model.21282_t
Valid prediction for Augustus_model.g8293.t1
Valid prediction for Augustus_model.g8287.t1
Valid prediction for GeneMark_model.21301_t
Valid prediction for snap_scaffold_5-snap.1585-T1
Valid prediction for snap_scaffold_5-snap.1568-T1
Valid prediction for Augustus_model.g8297.t1
Valid prediction for snap_scaffold_5-snap.1573-T1
Valid prediction for CodingQuarry_transcript_52008-T1
Valid prediction for GlimmerHMM_glimmerT_12528-T1
Valid prediction for GlimmerHMM_glimmerT_12510-T1
Valid prediction for GlimmerHMM_glimmerT_12534-T1
Valid prediction for snap_scaffold_5-snap.1565-T1
Valid prediction for GlimmerHMM_glimmerT_12520-T1
Valid prediction for snap_scaffold_5-snap.1567-T1
Valid prediction for HiQ_model.g8294.t1
Valid prediction for GeneMark_model.21288_t
Valid prediction for GlimmerHMM_glimmerT_12532-T1
Valid prediction for GeneMark_model.21296_t
Couldn't classify 55528, 56101
Sorry, prediction pasa_asmbl_45581.p1 fails validation.
(CAT)	 TT	55528-56101	GT	AGG
(GGG)	 AG	56329-57188	AC	AAA
-recovered pasa_asmbl_45581.p1, terminal, 56329, 57188
Valid prediction for GeneMark_model.21284_t
Valid prediction for snap_scaffold_5-snap.1564-T1
Valid prediction for GlimmerHMM_glimmerT_12514-T1
Valid prediction for snap_scaffold_5-snap.1572-T1
Valid prediction for snap_scaffold_5-snap.1578-T1
Valid prediction for snap_scaffold_5-snap.1570-T1
Valid prediction for GeneMark_model.21285_t
Valid prediction for HiQ_model.g8290.t1
Valid prediction for pasa_asmbl_45580.p1
Valid prediction for GeneMark_model.21305_t
Valid prediction for Augustus_model.g8292.t1
Valid prediction for snap_scaffold_5-snap.1582-T1
Valid prediction for GeneMark_model.21291_t
Valid prediction for snap_scaffold_5-snap.1581-T1
Valid prediction for GlimmerHMM_glimmerT_12533-T1
Valid prediction for snap_scaffold_5-snap.1580-T1
Valid prediction for snap_scaffold_5-snap.1563-T1
Valid prediction for GlimmerHMM_glimmerT_12536-T1
Valid prediction for GeneMark_model.21307_t
Valid prediction for GlimmerHMM_glimmerT_12527-T1
Valid prediction for GeneMark_model.21309_t
Valid prediction for GlimmerHMM_glimmerT_12506-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20845, rend_intergenic: 11064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39684, rend_intergenic: 36635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58054, rend_intergenic: 53827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182422
-exon list size: 435


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.7    
3.0    
3.2    
3.4    
3.7    
3.9    
4.1    
4.3    
4.6    
4.8    
5.0    
5.3    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.9    
7.1    
7.3    
7.6    
7.8    
8.0    
8.2    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.8    
10.1    
10.3    
10.5    
10.8    
11.0    
11.2    
11.4    
11.7    
11.9    
12.1    
12.4    
12.6    
12.8    
13.0    
13.3    
13.5    
13.7    
14.0    
14.2    
14.4    
14.6    
14.9    
15.1    
15.3    
15.6    
15.8    
16.0    
16.2    
16.5    
16.7    
16.9    
17.2    
17.4    
17.6    
17.8    
18.1    
18.3    
18.5    
18.8    
19.0    
19.2    
19.5    
19.7    
19.9    
20.1    
20.4    
20.6    
20.8    
21.1    
21.3    
21.5    
21.7    
22.0    
22.2    
22.4    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.5    
26.8    
27.0    
27.2    
27.5    
27.7    
27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.5    
45.8    
46.0    
46.2    
46.5    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.1    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
51.9    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.5    
53.8    
54.0    
54.2    
54.5    
54.7    
54.9    
55.1    
55.4    
55.6    
55.8    
56.1    
56.3    
56.5    
56.8    
57.0    
57.2    
57.4    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.0    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.9    
61.1    
61.3    
61.6    
61.8    
62.0    
62.2    
62.5    
62.7    
62.9    
63.2    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.4    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.0    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.6    
68.9    
69.1    
69.3    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
70.9    
71.2    
71.4    
71.6    
71.9    
72.1    
72.3    
72.5    
72.8    
73.0    
73.2    
73.5    
73.7    
73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.4    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 20845, rend_intergenic: 11064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39684, rend_intergenic: 36635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58054, rend_intergenic: 53827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12538
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11960
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11259
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11152
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support